GPMDB Data Sources

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#Rice RH, Xia Y, Alvarado RJ, Phinney BS,  (2010) &quot;Proteomic analysis of human nail plate.&quot; <i>J Proteome Res</i> <b>9</b>(12):6752&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20939611 20939611]; doi: [https://dx.doi.org/10.1021/pr1009349 10.1021/pr1009349]; GPMDB: [http://gpmdb.org/data/keyword/20939611 40].
#Rice RH, Xia Y, Alvarado RJ, Phinney BS,  (2010) &quot;Proteomic analysis of human nail plate.&quot; <i>J Proteome Res</i> <b>9</b>(12):6752&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20939611 20939611]; doi: [https://dx.doi.org/10.1021/pr1009349 10.1021/pr1009349]; GPMDB: [http://gpmdb.org/data/keyword/20939611 40].
#Khositseth S, Pisitkun T, Slentz DH, Wang G, Hoffert JD, Knepper MA, Yu MJ,  (2011) &quot;Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(1):M110.004036; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20940332 20940332]; doi: [https://dx.doi.org/10.1074/mcp.M110.004036 10.1074/mcp.M110.004036]; GPMDB: [http://gpmdb.org/data/keyword/20940332 5].
#Khositseth S, Pisitkun T, Slentz DH, Wang G, Hoffert JD, Knepper MA, Yu MJ,  (2011) &quot;Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(1):M110.004036; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20940332 20940332]; doi: [https://dx.doi.org/10.1074/mcp.M110.004036 10.1074/mcp.M110.004036]; GPMDB: [http://gpmdb.org/data/keyword/20940332 5].
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#Bowyer PW, Simon GM, Cravatt BF, Bogyo M,  (2011) &quot;Global profiling of proteolysis during rupture of Plasmodium falciparum from the host erythrocyte.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(5):M110.001636; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20943600 20943600]; doi: [https://dx.doi.org/10.1074/mcp.M110.001636 10.1074/mcp.M110.001636]; GPMDB: [http://gpmdb.org/data/keyword/20943600 760].
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#Dedieu A, Gaillard JC, Pourcher T, Darrouzet E, Armengaud J,  (2011) &quot;Revisiting iodination sites in thyroglobulin with an organ-oriented shotgun strategy.&quot; <i>J Biol Chem</i> <b>286</b>(1):259&ndash;69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20978121 20978121]; doi: [https://dx.doi.org/10.1074/jbc.M110.159483 10.1074/jbc.M110.159483]; GPMDB: [http://gpmdb.org/data/keyword/20978121 14].
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#Bartke T, Vermeulen M, Xhemalce B, Robson SC, Mann M, Kouzarides T,  (2010) &quot;Nucleosome-interacting proteins regulated by DNA and histone methylation.&quot; <i>Cell</i> <b>143</b>(3):470&ndash;84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21029866 21029866]; doi: [https://dx.doi.org/10.1016/j.cell.2010.10.012 10.1016/j.cell.2010.10.012]; GPMDB: [http://gpmdb.org/data/keyword/21029866 160].
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#de Souza GA, Arntzen M&Oslash;, Fortuin S, Sch&uuml;rch AC, M&aring;len H, McEvoy CR, van Soolingen D, Thiede B, Warren RM, Wiker HG,  (2011) &quot;Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(1):M110.002527; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21030493 21030493]; doi: [https://dx.doi.org/10.1074/mcp.M110.002527 10.1074/mcp.M110.002527]; GPMDB: [http://gpmdb.org/data/keyword/21030493 6].
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#Murray CI, Kane LA, Uhrigshardt H, Wang SB, Van Eyk JE,  (2011) &quot;Site-mapping of in vitro S-nitrosation in cardiac mitochondria: implications for cardioprotection.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.004721; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21036925 21036925]; doi: [https://dx.doi.org/10.1074/mcp.M110.004721 10.1074/mcp.M110.004721]; GPMDB: [http://gpmdb.org/data/keyword/21036925 36].
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#Walther DM, Mann M,  (2011) &quot;Accurate quantification of more than 4000 mouse tissue proteins reveals minimal proteome changes during aging.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(2):M110.004523; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21048193 21048193]; doi: [https://dx.doi.org/10.1074/mcp.M110.004523 10.1074/mcp.M110.004523]; GPMDB: [http://gpmdb.org/data/keyword/21048193 119].
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#Murphy JP, Pinto DM,  (2011) &quot;Targeted proteomic analysis of glycolysis in cancer cells.&quot; <i>J Proteome Res</i> <b>10</b>(2):604&ndash;13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21058741 21058741]; doi: [https://dx.doi.org/10.1021/pr100774f 10.1021/pr100774f]; GPMDB: [http://gpmdb.org/data/keyword/21058741 1].
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#Li YF, Arnold RJ, Tang H, Radivojac P,  (2010) &quot;The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics.&quot; <i>J Proteome Res</i> <b>9</b>(12):6288&ndash;97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21067214 21067214]; doi: [https://dx.doi.org/10.1021/pr1005586 10.1021/pr1005586]; GPMDB: [http://gpmdb.org/data/keyword/21067214 20].
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#Vranakis I, De Bock PJ, Papadioti A, Tselentis Y, Gevaert K, Tsiotis G, Psaroulaki A,  (2011) &quot;Identification of potentially involved proteins in levofloxacin resistance mechanisms in Coxiella burnetii.&quot; <i>J Proteome Res</i> <b>10</b>(2):756&ndash;62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21070068 21070068]; doi: [https://dx.doi.org/10.1021/pr100906v 10.1021/pr100906v]; GPMDB: [http://gpmdb.org/data/keyword/21070068 1].
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#Angel TE, Luft BJ, Yang X, Nicora CD, Camp DG 2nd, Jacobs JM, Smith RD,  (2010) &quot;Proteome analysis of Borrelia burgdorferi response to environmental change.&quot; <i>PLoS One</i> <b>5</b>(11):e13800; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21072190 21072190]; doi: [https://dx.doi.org/10.1371/journal.pone.0013800 10.1371/journal.pone.0013800]; GPMDB: [http://gpmdb.org/data/keyword/21072190 70].
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#Majeran W, Friso G, Ponnala L, Connolly B, Huang M, Reidel E, Zhang C, Asakura Y, Bhuiyan NH, Sun Q, Turgeon R, van Wijk KJ,  (2010) &quot;Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize.&quot; <i>Plant Cell</i> <b>22</b>(11):3509&ndash;42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21081695 21081695]; doi: [https://dx.doi.org/10.1105/tpc.110.079764 10.1105/tpc.110.079764]; GPMDB: [http://gpmdb.org/data/keyword/21081695 453].
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#Valgepea K, Adamberg K, Nahku R, Lahtvee PJ, Arike L, Vilu R,  (2010) &quot;Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase.&quot; <i>BMC Syst Biol</i> <b>4</b>:166; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21122111 21122111]; doi: [https://dx.doi.org/10.1186/1752-0509-4-166 10.1186/1752-0509-4-166]; GPMDB: [http://gpmdb.org/data/keyword/21122111 22].
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#Helbig AO, Rosati S, Pijnappel PW, van Breukelen B, Timmers MH, Mohammed S, Slijper M, Heck AJ,  (2010) &quot;Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.&quot; <i>BMC Genomics</i> <b>11</b>:685; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21126336 21126336]; doi: [https://dx.doi.org/10.1186/1471-2164-11-685 10.1186/1471-2164-11-685]; GPMDB: [http://gpmdb.org/data/keyword/21126336 10].
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#Fan C, Fu Z, Su Q, Angelini DJ, Van Eyk J, Johns RA,  (2011) &quot;S100A11 mediates hypoxia-induced mitogenic factor (HIMF)-induced smooth muscle cell migration, vesicular exocytosis, and nuclear activation.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.000901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21139050 21139050]; doi: [https://dx.doi.org/10.1074/mcp.M110.000901 10.1074/mcp.M110.000901]; GPMDB: [http://gpmdb.org/data/keyword/21139050 13].
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#Skirycz A, Memmi S, De Bodt S, Maleux K, Obata T, Fernie AR, Devreese B, Inz&eacute; D,  (2011) &quot;A reciprocal 15N-labeling proteomic analysis of expanding Arabidopsis leaves subjected to osmotic stress indicates importance of mitochondria in preserving plastid functions.&quot; <i>J Proteome Res</i> <b>10</b>(3):1018&ndash;29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21142212 21142212]; doi: [https://dx.doi.org/10.1021/pr100785n 10.1021/pr100785n]; GPMDB: [http://gpmdb.org/data/keyword/21142212 476].
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#Mestdagh P, Bostr&ouml;m AK, Impens F, Fredlund E, Van Peer G, De Antonellis P, von Stedingk K, Ghesqui&egrave;re B, Schulte S, Dews M, Thomas-Tikhonenko A, Schulte JH, Zollo M, Schramm A, Gevaert K, Axelson H, Speleman F, Vandesompele J,  (2010) &quot;The miR-17-92 microRNA cluster regulates multiple components of the TGF-&beta; pathway in neuroblastoma.&quot; <i>Mol Cell</i> <b>40</b>(5):762&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21145484 21145484]; doi: [https://dx.doi.org/10.1016/j.molcel.2010.11.038 10.1016/j.molcel.2010.11.038]; GPMDB: [http://gpmdb.org/data/keyword/21145484 1].
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#Li QR, Xing XB, Chen TT, Li RX, Dai J, Sheng QH, Xin SM, Zhu LL, Jin Y, Pei G, Kang JH, Li YX, Zeng R,  (2011) &quot;Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(4):M110.001750; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21149613 21149613]; doi: [https://dx.doi.org/10.1074/mcp.M110.001750 10.1074/mcp.M110.001750]; GPMDB: [http://gpmdb.org/data/keyword/21149613 12].
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#Ito J, Batth TS, Petzold CJ, Redding-Johanson AM, Mukhopadhyay A, Verboom R, Meyer EH, Millar AH, Heazlewood JL,  (2011) &quot;Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism.&quot; <i>J Proteome Res</i> <b>10</b>(4):1571&ndash;82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21166475 21166475]; doi: [https://dx.doi.org/10.1021/pr1009433 10.1021/pr1009433]; GPMDB: [http://gpmdb.org/data/keyword/21166475 3].
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#Lee JE, Sweredoski MJ, Graham RL, Kolawa NJ, Smith GT, Hess S, Deshaies RJ,  (2011) &quot;The steady-state repertoire of human SCF ubiquitin ligase complexes does not require ongoing Nedd8 conjugation.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(5):M110.006460; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21169563 21169563]; doi: [https://dx.doi.org/10.1074/mcp.M110.006460 10.1074/mcp.M110.006460]; GPMDB: [http://gpmdb.org/data/keyword/21169563 41].
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#Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Vill&eacute;n J, Haas W, Sowa ME, Gygi SP,  (2010) &quot;A tissue-specific atlas of mouse protein phosphorylation and expression.&quot; <i>Cell</i> <b>143</b>(7):1174&ndash;89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21183079 21183079]; doi: [https://dx.doi.org/10.1016/j.cell.2010.12.001 10.1016/j.cell.2010.12.001]; GPMDB: [http://gpmdb.org/data/keyword/21183079 313].
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#Brockmeyer C, Paster W, Pepper D, Tan CP, Trudgian DC, McGowan S, Fu G, Gascoigne NR, Acuto O, Salek M,  (2011) &quot;T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component.&quot; <i>J Biol Chem</i> <b>286</b>(9):7535&ndash;47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189249 21189249]; doi: [https://dx.doi.org/10.1074/jbc.M110.201236 10.1074/jbc.M110.201236]; GPMDB: [http://gpmdb.org/data/keyword/21189249 4].
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#Manes NP, Dong L, Zhou W, Du X, Reghu N, Kool AC, Choi D, Bailey CL, Petricoin EF 3rd, Liotta LA, Popov SG,  (2011) &quot;Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.000927; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189417 21189417]; doi: [https://dx.doi.org/10.1074/mcp.M110.000927 10.1074/mcp.M110.000927]; GPMDB: [http://gpmdb.org/data/keyword/21189417 66].
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#Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M,  (2011) &quot;Time-resolved quantitative proteome analysis of in vivo intestinal development.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.005231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21191033 21191033]; doi: [https://dx.doi.org/10.1074/mcp.M110.005231 10.1074/mcp.M110.005231]; GPMDB: [http://gpmdb.org/data/keyword/21191033 48].
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#Singh SK, Lakshmi MG, Saxena S, Swamy CV, Idris MM,  (2011) &quot;Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis.&quot; <i>J Sep Sci</i> <b>34</b>(2):225&ndash;32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21246729 21246729]; doi: [https://dx.doi.org/10.1002/jssc.201000626 10.1002/jssc.201000626]; GPMDB: [http://gpmdb.org/data/keyword/21246729 17].
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#Bantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, D&uuml;mpelfeld B, Eberhard D, Huthmacher C, Mathieson T, Poeckel D, Reader V, Strunk K, Sweetman G, Kruse U, Neubauer G, Ramsden NG, Drewes G,  (2011) &quot;Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes.&quot; <i>Nat Biotechnol</i> <b>29</b>(3):255&ndash;65; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21258344 21258344]; doi: [https://dx.doi.org/10.1038/nbt.1759 10.1038/nbt.1759]; GPMDB: [http://gpmdb.org/data/keyword/21258344 128].
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#Baerenfaller K, Hirsch-Hoffmann M, Svozil J, Hull R, Russenberger D, Bischof S, Lu Q, Gruissem W, Baginsky S,  (2011) &quot;pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.&quot; <i>Integr Biol (Camb)</i> <b>3</b>(3):225&ndash;37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21264403 21264403]; doi: [https://dx.doi.org/10.1039/c0ib00078g 10.1039/c0ib00078g]; GPMDB: [http://gpmdb.org/data/keyword/21264403 64].
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#Otto A, Bernhardt J, Meyer H, Schaffer M, Herbst FA, Siebourg J, M&auml;der U, Lalk M, Hecker M, Becher D,  (2010) &quot;Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis.&quot; <i>Nat Commun</i> <b>1</b>:137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21266987 21266987]; doi: [https://dx.doi.org/10.1038/ncomms1137 10.1038/ncomms1137]; GPMDB: [http://gpmdb.org/data/keyword/21266987 76].
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#Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, B&uuml;rckst&uuml;mmer T, Bennett KL, Superti-Furga G, Colinge J,  (2011) &quot;Initial characterization of the human central proteome.&quot; <i>BMC Syst Biol</i> <b>5</b>:17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21269460 21269460]; doi: [https://dx.doi.org/10.1186/1752-0509-5-17 10.1186/1752-0509-5-17]; GPMDB: [http://gpmdb.org/data/keyword/21269460 99].
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#Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fav&eacute; MJ, Fernandes V, Gibson JD, Graur D, Gronenberg W, Grubbs KJ, Hagen DE, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND, Viljakainen L, Wolschin F, Gadau J,  (2011) &quot;Draft genome of the red harvester ant Pogonomyrmex barbatus.&quot; <i>Proc Natl Acad Sci U S A</i> <b>108</b>(14):5667&ndash;72; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21282651 21282651]; doi: [https://dx.doi.org/10.1073/pnas.1007901108 10.1073/pnas.1007901108]; GPMDB: [http://gpmdb.org/data/keyword/21282651 2].
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#Michalski A, Cox J, Mann M,  (2011) &quot;More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.&quot; <i>J Proteome Res</i> <b>10</b>(4):1785&ndash;93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21309581 21309581]; doi: [https://dx.doi.org/10.1021/pr101060v 10.1021/pr101060v]; GPMDB: [http://gpmdb.org/data/keyword/21309581 3].
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#Lahtvee PJ, Adamberg K, Arike L, Nahku R, Aller K, Vilu R,  (2011) &quot;Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates.&quot; <i>Microb Cell Fact</i> <b>10</b>:12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21349178 21349178]; doi: [https://dx.doi.org/10.1186/1475-2859-10-12 10.1186/1475-2859-10-12]; GPMDB: [http://gpmdb.org/data/keyword/21349178 64].
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#Paul D, Kumar R, Nanduri B, French T, Pendarvis K, Brown A, Lawrence ML, Burgess SC,  (2011) &quot;Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions.&quot; <i>PLoS One</i> <b>6</b>(2):e17111; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21386900 21386900]; doi: [https://dx.doi.org/10.1371/journal.pone.0017111 10.1371/journal.pone.0017111]; GPMDB: [http://gpmdb.org/data/keyword/21386900 1].
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#Li J, Su Z, Ma ZQ, Slebos RJ, Halvey P, Tabb DL, Liebler DC, Pao W, Zhang B,  (2011) &quot;A bioinformatics workflow for variant peptide detection in shotgun proteomics.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(5):M110.006536; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21389108 21389108]; doi: [https://dx.doi.org/10.1074/mcp.M110.006536 10.1074/mcp.M110.006536]; GPMDB: [http://gpmdb.org/data/keyword/21389108 59].
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#Frese CK, Altelaar AF, Hennrich ML, Nolting D, Zeller M, Griep-Raming J, Heck AJ, Mohammed S,  (2011) &quot;Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos.&quot; <i>J Proteome Res</i> <b>10</b>(5):2377&ndash;88; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21413819 21413819]; doi: [https://dx.doi.org/10.1021/pr1011729 10.1021/pr1011729]; GPMDB: [http://gpmdb.org/data/keyword/21413819 73].
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#Poliakov A, Russell CW, Ponnala L, Hoops HJ, Sun Q, Douglas AE, van Wijk KJ,  (2011) &quot;Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(6):M110.007039; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21421797 21421797]; doi: [https://dx.doi.org/10.1074/mcp.M110.007039 10.1074/mcp.M110.007039]; GPMDB: [http://gpmdb.org/data/keyword/21421797 148].
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#Di Palma S, Boersema PJ, Heck AJ, Mohammed S,  (2011) &quot;Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis.&quot; <i>Anal Chem</i> <b>83</b>(9):3440&ndash;7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21443167 21443167]; doi: [https://dx.doi.org/10.1021/ac103312e 10.1021/ac103312e]; GPMDB: [http://gpmdb.org/data/keyword/21443167 4].
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#Jagannadham MV, Abou-Eladab EF, Kulkarni HM,  (2011) &quot;Identification of outer membrane proteins from an Antarctic bacterium Pseudomonas syringae Lz4W.&quot; <i>Mol Cell Proteomics</i> <b>10</b>(6):M110.004549; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21447709 21447709]; doi: [https://dx.doi.org/10.1074/mcp.M110.004549 10.1074/mcp.M110.004549]; GPMDB: [http://gpmdb.org/data/keyword/21447709 14].
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#Chik JK, Schriemer DC, Childs SJ, McGhee JD,  (2011) &quot;Proteome of the Caenorhabditis elegans oocyte.&quot; <i>J Proteome Res</i> <b>10</b>(5):2300&ndash;5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21452892 21452892]; doi: [https://dx.doi.org/10.1021/pr101124f 10.1021/pr101124f]; GPMDB: [http://gpmdb.org/data/keyword/21452892 125].
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#Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T,  (2011) &quot;Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and &quot;resurrected&quot; pseudogenes in the mouse genome.&quot; <i>Genome Res</i> <b>21</b>(5):756&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21460061 21460061]; doi: [https://dx.doi.org/10.1101/gr.114272.110 10.1101/gr.114272.110]; GPMDB: [http://gpmdb.org/data/keyword/21460061 3].
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#Elschenbroich S, Ignatchenko V, Clarke B, Kalloger SE, Boutros PC, Gramolini AO, Shaw P, Jurisica I, Kislinger T,  (2011) &quot;In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry.&quot; <i>J Proteome Res</i> <b>10</b>(5):2286&ndash;99; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21491939 21491939]; doi: [https://dx.doi.org/10.1021/pr1011087 10.1021/pr1011087]; GPMDB: [http://gpmdb.org/data/keyword/21491939 210].
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#Malmstr&ouml;m J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmstr&ouml;m L, Bj&ouml;rck L,  (2012) &quot;Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics.&quot; <i>J Biol Chem</i> <b>287</b>(2):1415&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22117078 22117078]; doi: [https://dx.doi.org/10.1074/jbc.M111.267674 10.1074/jbc.M111.267674]; GPMDB: [http://gpmdb.org/data/keyword/22117078 41].
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#Christianson JC, Olzmann JA, Shaler TA, Sowa ME, Bennett EJ, Richter CM, Tyler RE, Greenblatt EJ, Harper JW, Kopito RR,  (2011) &quot;Defining human ERAD networks through an integrative mapping strategy.&quot; <i>Nat Cell Biol</i> <b>14</b>(1):93&ndash;105; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22119785 22119785]; doi: [https://dx.doi.org/10.1038/ncb2383 10.1038/ncb2383]; GPMDB: [http://gpmdb.org/data/keyword/22119785 94].
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#Journet A, Klein G, Brugi&egrave;re S, Vandenbrouck Y, Chapel A, Kieffer S, Bruley C, Masselon C, Aubry L,  (2012) &quot;Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry.&quot; <i>Proteomics</i> <b>12</b>(2):241&ndash;5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22120990 22120990]; doi: [https://dx.doi.org/10.1002/pmic.201100313 10.1002/pmic.201100313]; GPMDB: [http://gpmdb.org/data/keyword/22120990 1].
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#Murray CI, Uhrigshardt H, O&#39;Meally RN, Cole RN, Van Eyk JE,  (2012) &quot;Identification and quantification of S-nitrosylation by cysteine reactive tandem mass tag switch assay.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(2):M111.013441; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22126794 22126794]; doi: [https://dx.doi.org/10.1074/mcp.M111.013441 10.1074/mcp.M111.013441]; GPMDB: [http://gpmdb.org/data/keyword/22126794 3].
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#Bischof S, Baerenfaller K, Wildhaber T, Troesch R, Vidi PA, Roschitzki B, Hirsch-Hoffmann M, Hennig L, Kessler F, Gruissem W, Baginsky S,  (2011) &quot;Plastid proteome assembly without Toc159: photosynthetic protein import and accumulation of N-acetylated plastid precursor proteins.&quot; <i>Plant Cell</i> <b>23</b>(11):3911&ndash;28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22128122 22128122]; doi: [https://dx.doi.org/10.1105/tpc.111.092882 10.1105/tpc.111.092882]; GPMDB: [http://gpmdb.org/data/keyword/22128122 6].
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#Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A,  (2012) &quot;Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry.&quot; <i>J Proteome Res</i> <b>11</b>(1):247&ndash;60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22129275 22129275]; doi: [https://dx.doi.org/10.1021/pr200827k 10.1021/pr200827k]; GPMDB: [http://gpmdb.org/data/keyword/22129275 70].
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#Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, STREAM Consortium, Wohlleben W, Rodr&iacute;guez-Garc&iacute;a A, Mart&iacute;n JF, Burroughs NJ, Wellington EM, Smith MC,  (2012) &quot;Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(2):M111.013797; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22147733 22147733]; doi: [https://dx.doi.org/10.1074/mcp.M111.013797 10.1074/mcp.M111.013797]; GPMDB: [http://gpmdb.org/data/keyword/22147733 64].
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#Choi DS, Yang JS, Choi EJ, Jang SC, Park S, Kim OY, Hwang D, Kim KP, Kim YK, Kim S, Gho YS,  (2012) &quot;The protein interaction network of extracellular vesicles derived from human colorectal cancer cells.&quot; <i>J Proteome Res</i> <b>11</b>(2):1144&ndash;51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22149170 22149170]; doi: [https://dx.doi.org/10.1021/pr200842h 10.1021/pr200842h]; GPMDB: [http://gpmdb.org/data/keyword/22149170 1].
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#Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO,  (2012) &quot;The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(4):M111.014647; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22159717 22159717]; doi: [https://dx.doi.org/10.1074/mcp.M111.014647 10.1074/mcp.M111.014647]; GPMDB: [http://gpmdb.org/data/keyword/22159717 98].
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#Michalski A, Damoc E, Lange O, Denisov E, Nolting D, M&uuml;ller M, Viner R, Schwartz J, Remes P, Belford M, Dunyach JJ, Cox J, Horning S, Mann M, Makarov A,  (2012) &quot;Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):O111.013698; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22159718 22159718]; doi: [https://dx.doi.org/10.1074/mcp.O111.013698 10.1074/mcp.O111.013698]; GPMDB: [http://gpmdb.org/data/keyword/22159718 22].
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#Martins-de-Souza D, Guest PC, Guest FL, Bauder C, Rahmoune H, Pietsch S, Roeber S, Kretzschmar H, Mann D, Baborie A, Bahn S,  (2012) &quot;Characterization of the human primary visual cortex and cerebellum proteomes using shotgun mass spectrometry-data-independent analyses.&quot; <i>Proteomics</i> <b>12</b>(3):500&ndash;4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22162416 22162416]; doi: [https://dx.doi.org/10.1002/pmic.201100476 10.1002/pmic.201100476]; GPMDB: [http://gpmdb.org/data/keyword/22162416 26].
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#Burkhart JM, Schumbrutzki C, Wortelkamp S, Sickmann A, Zahedi RP,  (2012) &quot;Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics.&quot; <i>J Proteomics</i> <b>75</b>(4):1454&ndash;62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22166745 22166745]; doi: [https://dx.doi.org/10.1016/j.jprot.2011.11.016 10.1016/j.jprot.2011.11.016]; GPMDB: [http://gpmdb.org/data/keyword/22166745 1].
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#Sharma K, Vabulas RM, Macek B, Pinkert S, Cox J, Mann M, Hartl FU,  (2012) &quot;Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):M111.014654; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22167270 22167270]; doi: [https://dx.doi.org/10.1074/mcp.M111.014654 10.1074/mcp.M111.014654]; GPMDB: [http://gpmdb.org/data/keyword/22167270 41].
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#Graumann J, Scheltema RA, Zhang Y, Cox J, Mann M,  (2012) &quot;A framework for intelligent data acquisition and real-time database searching for shotgun proteomics.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):M111.013185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22171319 22171319]; doi: [https://dx.doi.org/10.1074/mcp.M111.013185 10.1074/mcp.M111.013185]; GPMDB: [http://gpmdb.org/data/keyword/22171319 13].
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#Dresang LR, Teuton JR, Feng H, Jacobs JM, Camp DG 2nd, Purvine SO, Gritsenko MA, Li Z, Smith RD, Sugden B, Moore PS, Chang Y,  (2011) &quot;Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes.&quot; <i>BMC Genomics</i> <b>12</b>:625; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22185355 22185355]; doi: [https://dx.doi.org/10.1186/1471-2164-12-625 10.1186/1471-2164-12-625]; GPMDB: [http://gpmdb.org/data/keyword/22185355 1].
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#Batruch I, Smith CR, Mullen BJ, Grober E, Lo KC, Diamandis EP, Jarvi KA,  (2012) &quot;Analysis of seminal plasma from patients with non-obstructive azoospermia and identification of candidate biomarkers of male infertility.&quot; <i>J Proteome Res</i> <b>11</b>(3):1503&ndash;11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22188163 22188163]; doi: [https://dx.doi.org/10.1021/pr200812p 10.1021/pr200812p]; GPMDB: [http://gpmdb.org/data/keyword/22188163 12].
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#Altelaar AF, Navarro D, Boekhorst J, van Breukelen B, Snel B, Mohammed S, Heck AJ,  (2012) &quot;Database independent proteomics analysis of the ostrich and human proteome.&quot; <i>Proc Natl Acad Sci U S A</i> <b>109</b>(2):407&ndash;12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22198768 22198768]; doi: [https://dx.doi.org/10.1073/pnas.1108399108 10.1073/pnas.1108399108]; GPMDB: [http://gpmdb.org/data/keyword/22198768 21].
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#Oppermann FS, Grundner-Culemann K, Kumar C, Gruss OJ, Jallepalli PV, Daub H,  (2012) &quot;Combination of chemical genetics and phosphoproteomics for kinase signaling analysis enables confident identification of cellular downstream targets.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(4):O111.012351; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22199227 22199227]; doi: [https://dx.doi.org/10.1074/mcp.O111.012351 10.1074/mcp.O111.012351]; GPMDB: [http://gpmdb.org/data/keyword/22199227 96].
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#Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA,  (2012) &quot;iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(6):M111.014423; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22210691 22210691]; doi: [https://dx.doi.org/10.1074/mcp.M111.014423 10.1074/mcp.M111.014423]; GPMDB: [http://gpmdb.org/data/keyword/22210691 32].
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#Elmore JM, Liu J, Smith B, Phinney B, Coaker G,  (2012) &quot;Quantitative proteomics reveals dynamic changes in the plasma membrane during Arabidopsis immune signaling.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(4):M111.014555; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22215637 22215637]; doi: [https://dx.doi.org/10.1074/mcp.M111.014555 10.1074/mcp.M111.014555]; GPMDB: [http://gpmdb.org/data/keyword/22215637 90].
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#K&ouml;nig S, Nimtz M, Scheiter M, Ljunggren HG, Bryceson YT, J&auml;nsch L,  (2012) &quot;Kinome analysis of receptor-induced phosphorylation in human natural killer cells.&quot; <i>PLoS One</i> <b>7</b>(1):e29672; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22238634 22238634]; doi: [https://dx.doi.org/10.1371/journal.pone.0029672 10.1371/journal.pone.0029672]; GPMDB: [http://gpmdb.org/data/keyword/22238634 3].
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#Al-Hakim AK, Bashkurov M, Gingras AC, Durocher D, Pelletier L,  (2012) &quot;Interaction proteomics identify NEURL4 and the HECT E3 ligase HERC2 as novel modulators of centrosome architecture.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(6):M111.014233; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22261722 22261722]; doi: [https://dx.doi.org/10.1074/mcp.M111.014233 10.1074/mcp.M111.014233]; GPMDB: [http://gpmdb.org/data/keyword/22261722 18].
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#Franklin S, Chen H, Mitchell-Jordan S, Ren S, Wang Y, Vondriska TM,  (2012) &quot;Quantitative analysis of the chromatin proteome in disease reveals remodeling principles and identifies high mobility group protein B2 as a regulator of hypertrophic growth.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(6):M111.014258; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22270000 22270000]; doi: [https://dx.doi.org/10.1074/mcp.M111.014258 10.1074/mcp.M111.014258]; GPMDB: [http://gpmdb.org/data/keyword/22270000 75].
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#Tauro BJ, Greening DW, Mathias RA, Ji H, Mathivanan S, Scott AM, Simpson RJ,  (2012) &quot;Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes.&quot; <i>Methods</i> <b>56</b>(2):293&ndash;304; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22285593 22285593]; doi: [https://dx.doi.org/10.1016/j.ymeth.2012.01.002 10.1016/j.ymeth.2012.01.002]; GPMDB: [http://gpmdb.org/data/keyword/22285593 163].
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#Schaab C, Geiger T, Stoehr G, Cox J, Mann M,  (2012) &quot;Analysis of high accuracy, quantitative proteomics data in the MaxQB database.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):M111.014068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22301388 22301388]; doi: [https://dx.doi.org/10.1074/mcp.M111.014068 10.1074/mcp.M111.014068]; GPMDB: [http://gpmdb.org/data/keyword/22301388 361].
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#Stokes MP, Farnsworth CL, Moritz A, Silva JC, Jia X, Lee KA, Guo A, Polakiewicz RD, Comb MJ,  (2012) &quot;PTMScan direct: identification and quantification of peptides from critical signaling proteins by immunoaffinity enrichment coupled with LC-MS/MS.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(5):187&ndash;201; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22322096 22322096]; doi: [https://dx.doi.org/10.1074/mcp.M111.015883 10.1074/mcp.M111.015883]; GPMDB: [http://gpmdb.org/data/keyword/22322096 24].
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#Chen ZW, Fuchs K, Sieghart W, Townsend RR, Evers AS,  (2012) &quot;Deep amino acid sequencing of native brain GABAA receptors using high-resolution mass spectrometry.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(1):M111.011445; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22338125 22338125]; GPMDB: [http://gpmdb.org/data/keyword/22338125 16].
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#Sandalakis V, Psaroulaki A, De Bock PJ, Christidou A, Gevaert K, Tsiotis G, Tselentis Y,  (2012) &quot;Investigation of rifampicin resistance mechanisms in Brucella abortus using MS-driven comparative proteomics.&quot; <i>J Proteome Res</i> <b>11</b>(4):2374&ndash;85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22360387 22360387]; doi: [https://dx.doi.org/10.1021/pr201122w 10.1021/pr201122w]; GPMDB: [http://gpmdb.org/data/keyword/22360387 1].
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#Geiger T, Madden SF, Gallagher WM, Cox J, Mann M,  (2012) &quot;Proteomic portrait of human breast cancer progression identifies novel prognostic markers.&quot; <i>Cancer Res</i> <b>72</b>(9):2428&ndash;39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22414580 22414580]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-11-3711 10.1158/0008-5472.CAN-11-3711]; GPMDB: [http://gpmdb.org/data/keyword/22414580 420].
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#Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NS,  (2012) &quot;Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry.&quot; <i>Mol Syst Biol</i> <b>8</b>:573; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22415777 22415777]; doi: [https://dx.doi.org/10.1038/msb.2012.5 10.1038/msb.2012.5]; GPMDB: [http://gpmdb.org/data/keyword/22415777 62].
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#Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O&#39;Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M,  (2012) &quot;Personal omics profiling reveals dynamic molecular and medical phenotypes.&quot; <i>Cell</i> <b>148</b>(6):1293&ndash;307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22424236 22424236]; doi: [https://dx.doi.org/10.1016/j.cell.2012.02.009 10.1016/j.cell.2012.02.009]; GPMDB: [http://gpmdb.org/data/keyword/22424236 165].
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#Vranakis I, De Bock PJ, Papadioti A, Tselentis Y, Gevaert K, Tsiotis G, Psaroulaki A,  (2012) &quot;Quantitative proteome profiling of C. burnetii under tetracycline stress conditions.&quot; <i>PLoS One</i> <b>7</b>(3):e33599; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22438959 22438959]; doi: [https://dx.doi.org/10.1371/journal.pone.0033599 10.1371/journal.pone.0033599]; GPMDB: [http://gpmdb.org/data/keyword/22438959 2].
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#Deeb SJ, D&#39;Souza RC, Cox J, Schmidt-Supprian M, Mann M,  (2012) &quot;Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(5):77&ndash;89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22442255 22442255]; doi: [https://dx.doi.org/10.1074/mcp.M111.015362 10.1074/mcp.M111.015362]; GPMDB: [http://gpmdb.org/data/keyword/22442255 60].
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#Tondeleir D, Lambrechts A, M&uuml;ller M, Jonckheere V, Doll T, Vandamme D, Bakkali K, Waterschoot D, Lemaistre M, Debeir O, Decaestecker C, Hinz B, Staes A, Timmerman E, Colaert N, Gevaert K, Vandekerckhove J, Ampe C,  (2012) &quot;Cells lacking &beta;-actin are genetically reprogrammed and maintain conditional migratory capacity.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(8):255&ndash;71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22448045 22448045]; doi: [https://dx.doi.org/10.1074/mcp.M111.015099 10.1074/mcp.M111.015099]; GPMDB: [http://gpmdb.org/data/keyword/22448045 2].
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#Schrimpe-Rutledge AC, Jones MB, Chauhan S, Purvine SO, Sanford JA, Monroe ME, Brewer HM, Payne SH, Ansong C, Frank BC, Smith RD, Peterson SN, Motin VL, Adkins JN,  (2012) &quot;Comparative omics-driven genome annotation refinement: application across Yersiniae.&quot; <i>PLoS One</i> <b>7</b>(3):e33903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22479471 22479471]; doi: [https://dx.doi.org/10.1371/journal.pone.0033903 10.1371/journal.pone.0033903]; GPMDB: [http://gpmdb.org/data/keyword/22479471 226].
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#Franz-Wachtel M, Eisler SA, Krug K, Wahl S, Carpy A, Nordheim A, Pfizenmaier K, Hausser A, Macek B,  (2012) &quot;Global detection of protein kinase D-dependent phosphorylation events in nocodazole-treated human cells.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(5):160&ndash;70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22496350 22496350]; doi: [https://dx.doi.org/10.1074/mcp.M111.016014 10.1074/mcp.M111.016014]; GPMDB: [http://gpmdb.org/data/keyword/22496350 18].
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#Ferrando IM, Chaerkady R, Zhong J, Molina H, Jacob HK, Herbst-Robinson K, Dancy BM, Katju V, Bose R, Zhang J, Pandey A, Cole PA,  (2012) &quot;Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(8):355&ndash;69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22499769 22499769]; doi: [https://dx.doi.org/10.1074/mcp.M111.015750 10.1074/mcp.M111.015750]; GPMDB: [http://gpmdb.org/data/keyword/22499769 7].
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#Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA,  (2012) &quot;Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(5):148&ndash;59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22505724 22505724]; doi: [https://dx.doi.org/10.1074/mcp.M111.016857 10.1074/mcp.M111.016857]; GPMDB: [http://gpmdb.org/data/keyword/22505724 113].
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#Yao L, Lao W, Zhang Y, Tang X, Hu X, He C, Hu X, Xu LX,  (2012) &quot;Identification of EFEMP2 as a serum biomarker for the early detection of colorectal cancer with lectin affinity capture assisted secretome analysis of cultured fresh tissues.&quot; <i>J Proteome Res</i> <b>11</b>(6):3281&ndash;94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22506683 22506683]; doi: [https://dx.doi.org/10.1021/pr300020p 10.1021/pr300020p]; GPMDB: [http://gpmdb.org/data/keyword/22506683 12].
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#Fonslow BR, Niessen SM, Singh M, Wong CC, Xu T, Carvalho PC, Choi J, Park SK, Yates JR 3rd,  (2012) &quot;Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT.&quot; <i>J Proteome Res</i> <b>11</b>(5):2697&ndash;709; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22509746 22509746]; doi: [https://dx.doi.org/10.1021/pr300200x 10.1021/pr300200x]; GPMDB: [http://gpmdb.org/data/keyword/22509746 77].
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#Urbaniak MD, Guther ML, Ferguson MA,  (2012) &quot;Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages.&quot; <i>PLoS One</i> <b>7</b>(5):e36619; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22574199 22574199]; doi: [https://dx.doi.org/10.1371/journal.pone.0036619 10.1371/journal.pone.0036619]; GPMDB: [http://gpmdb.org/data/keyword/22574199 11].
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#Ivaldi C, Martin BR, Kieffer-Jaquinod S, Chapel A, Levade T, Garin J, Journet A,  (2012) &quot;Proteomic analysis of S-acylated proteins in human B cells reveals palmitoylation of the immune regulators CD20 and CD23.&quot; <i>PLoS One</i> <b>7</b>(5):e37187; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22615937 22615937]; doi: [https://dx.doi.org/10.1371/journal.pone.0037187 10.1371/journal.pone.0037187]; GPMDB: [http://gpmdb.org/data/keyword/22615937 2].
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#Byron A, Humphries JD, Craig SE, Knight D, Humphries MJ,  (2012) &quot;Proteomic analysis of &alpha;4&beta;1 integrin adhesion complexes reveals &alpha;-subunit-dependent protein recruitment.&quot; <i>Proteomics</i> <b>12</b>(13):2107&ndash;14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22623428 22623428]; doi: [https://dx.doi.org/10.1002/pmic.201100487 10.1002/pmic.201100487]; GPMDB: [http://gpmdb.org/data/keyword/22623428 18].
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#Pisitkun T, Gandolfo MT, Das S, Knepper MA, Bagnasco SM,  (2012) &quot;Application of systems biology principles to protein biomarker discovery: urinary exosomal proteome in renal transplantation.&quot; <i>Proteomics Clin Appl</i> <b>6</b>(5-6):268&ndash;78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22641613 22641613]; doi: [https://dx.doi.org/10.1002/prca.201100108 10.1002/prca.201100108]; GPMDB: [http://gpmdb.org/data/keyword/22641613 7].
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#Coffill CR, Muller PA, Oh HK, Neo SP, Hogue KA, Cheok CF, Vousden KH, Lane DP, Blackstock WP, Gunaratne J,  (2012) &quot;Mutant p53 interactome identifies nardilysin as a p53R273H-specific binding partner that promotes invasion.&quot; <i>EMBO Rep</i> <b>13</b>(7):638&ndash;44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22653443 22653443]; doi: [https://dx.doi.org/10.1038/embor.2012.74 10.1038/embor.2012.74]; GPMDB: [http://gpmdb.org/data/keyword/22653443 154].
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#Rose CM, Venkateshwaran M, Volkening JD, Grimsrud PA, Maeda J, Bailey DJ, Park K, Howes-Podoll M, den Os D, Yeun LH, Westphall MS, Sussman MR, An&eacute; JM, Coon JJ,  (2012) &quot;Rapid phosphoproteomic and transcriptomic changes in the rhizobia-legume symbiosis.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(9):724&ndash;44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22683509 22683509]; doi: [https://dx.doi.org/10.1074/mcp.M112.019208 10.1074/mcp.M112.019208]; GPMDB: [http://gpmdb.org/data/keyword/22683509 382].
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#Rashid ST, Humphries JD, Byron A, Dhar A, Askari JA, Selley JN, Knight D, Goldin RD, Thursz M, Humphries MJ,  (2012) &quot;Proteomic analysis of extracellular matrix from the hepatic stellate cell line LX-2 identifies CYR61 and Wnt-5a as novel constituents of fibrotic liver.&quot; <i>J Proteome Res</i> <b>11</b>(8):4052&ndash;64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22694338 22694338]; doi: [https://dx.doi.org/10.1021/pr3000927 10.1021/pr3000927]; GPMDB: [http://gpmdb.org/data/keyword/22694338 6].
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#Lindner SE, Swearingen KE, Harupa A, Vaughan AM, Sinnis P, Moritz RL, Kappe SH,  (2013) &quot;Total and putative surface proteomics of malaria parasite salivary gland sporozoites.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(5):1127&ndash;43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23325771 23325771]; doi: [https://dx.doi.org/10.1074/mcp.M112.024505 10.1074/mcp.M112.024505]; GPMDB: [http://gpmdb.org/data/keyword/23325771 72].
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#Cramer GR, Van Sluyter SC, Hopper DW, Pascovici D, Keighley T, Haynes PA,  (2013) &quot;Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit.&quot; <i>BMC Plant Biol</i> <b>13</b>:49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23514573 23514573]; doi: [https://dx.doi.org/10.1186/1471-2229-13-49 10.1186/1471-2229-13-49]; GPMDB: [http://gpmdb.org/data/keyword/23514573 96].
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#Cuello F, Shankar-Hari M, Mayr U, Yin X, Marshall M, Suna G, Willeit P, Langley SR, Jayawardhana T, Zeller T, Terblanche M, Shah AM, Mayr M,  (2014) &quot;Redox state of pentraxin 3 as a novel biomarker for resolution of inflammation and survival in sepsis.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(10):2545&ndash;57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24958171 24958171]; doi: [https://dx.doi.org/10.1074/mcp.M114.039446 10.1074/mcp.M114.039446]; GPMDB: [http://gpmdb.org/data/keyword/24958171 384].
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#de Graaf EL, Kaplon J, Zhou H, Heck AJ, Peeper DS, Altelaar AF,  (2014) &quot;Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(8):2089&ndash;100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24961811 24961811]; doi: [https://dx.doi.org/10.1074/mcp.M113.035436 10.1074/mcp.M113.035436]; GPMDB: [http://gpmdb.org/data/keyword/24961811 223].
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#Iesmantavicius V, Weinert BT, Choudhary C,  (2014) &quot;Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(8):1979&ndash;92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24961812 24961812]; doi: [https://dx.doi.org/10.1074/mcp.O113.035683 10.1074/mcp.O113.035683]; GPMDB: [http://gpmdb.org/data/keyword/24961812 71].
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#Milbradt J, Kraut A, Hutterer C, Sonntag E, Schmeiser C, Ferro M, Wagner S, Lenac T, Claus C, Pinkert S, Hamilton ST, Rawlinson WD, Sticht H, Cout&eacute; Y, Marschall M,  (2014) &quot;Proteomic analysis of the multimeric nuclear egress complex of human cytomegalovirus.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(8):2132&ndash;46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24969177 24969177]; doi: [https://dx.doi.org/10.1074/mcp.M113.035782 10.1074/mcp.M113.035782]; GPMDB: [http://gpmdb.org/data/keyword/24969177 24].
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#Fischer MG, Kelly I, Foster LJ, Suttle CA,  (2014) &quot;The virion of Cafeteria roenbergensis virus (CroV) contains a complex suite of proteins for transcription and DNA repair.&quot; <i>Virology</i> <b>466-467</b>:82&ndash;94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24973308 24973308]; doi: [https://dx.doi.org/10.1016/j.virol.2014.05.029 10.1016/j.virol.2014.05.029]; GPMDB: [http://gpmdb.org/data/keyword/24973308 10].
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#Chiva C, Ortega M, Sabid&oacute; E,  (2014) &quot;Influence of the digestion technique, protease, and missed cleavage peptides in protein quantitation.&quot; <i>J Proteome Res</i> <b>13</b>(9):3979&ndash;86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24986539 24986539]; doi: [https://dx.doi.org/10.1021/pr500294d 10.1021/pr500294d]; GPMDB: [http://gpmdb.org/data/keyword/24986539 89].
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#Uechi G, Sun Z, Schreiber EM, Halfter W, Balasubramani M,  (2014) &quot;Proteomic View of Basement Membranes from Human Retinal Blood Vessels, Inner Limiting Membranes, and Lens Capsules.&quot; <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24990792 24990792]; doi: [https://dx.doi.org/10.1021/pr5002065 10.1021/pr5002065]; GPMDB: [http://gpmdb.org/data/keyword/24990792 315].
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#Zhang H, Wu P, Chen F, Hao Y, Lao Y, Ren L, Sun L, Sun W, Wei H, Chan DW, Jiang Y, He F,  (2014) &quot;SILAC-based quantitative proteomic analysis of secretome between activated and reverted hepatic stellate cells.&quot; <i>Proteomics</i> <b>14</b>(17-18):1977&ndash;86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24995952 24995952]; doi: [https://dx.doi.org/10.1002/pmic.201300539 10.1002/pmic.201300539]; GPMDB: [http://gpmdb.org/data/keyword/24995952 30].
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#Pasillas MP, Shields S, Reilly R, Strnadel J, Behl C, Park R, Yates JR 3rd, Klemke R, Gonias SL, Coppinger JA,  (2015) &quot;Proteomic analysis reveals a role for Bcl2-associated athanogene 3 and major vault protein in resistance to apoptosis in senescent cells by regulating ERK1/2 activation.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(1):1&ndash;14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24997994 24997994]; doi: [https://dx.doi.org/10.1074/mcp.M114.037697 10.1074/mcp.M114.037697]; GPMDB: [http://gpmdb.org/data/keyword/24997994 51].
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#Chopra T, Hamelin R, Armand F, Chiappe D, Moniatte M, McKinney JD,  (2014) &quot;Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(11):3014&ndash;28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24997995 24997995]; doi: [https://dx.doi.org/10.1074/mcp.M113.034082 10.1074/mcp.M113.034082]; GPMDB: [http://gpmdb.org/data/keyword/24997995 28].
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#&Ouml;hman T, S&ouml;derholm S, Hintsanen P, V&auml;lim&auml;ki E, Lietz&eacute;n N, MacKintosh C, Aittokallio T, Matikainen S, Nyman TA,  (2014) &quot;Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(10):2604&ndash;17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24997996 24997996]; doi: [https://dx.doi.org/10.1074/mcp.M114.038968 10.1074/mcp.M114.038968]; GPMDB: [http://gpmdb.org/data/keyword/24997996 44].
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#Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND,  (2014) &quot;Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(10):2618&ndash;31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24997998 24997998]; doi: [https://dx.doi.org/10.1074/mcp.M114.040428 10.1074/mcp.M114.040428]; GPMDB: [http://gpmdb.org/data/keyword/24997998 8].
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#Savijoki K, Iivanainen A, Siljam&auml;ki P, Laine PK, Paulin L, Karonen T, Py&ouml;r&auml;l&auml; S, Kankainen M, Nyman TA, Salom&auml;ki T, Koskinen P, Holm L, Simojoki H, Taponen S, Sukura A, Kalkkinen N, Auvinen P, Varmanen P,  (2014) &quot;Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains.&quot; <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25014494 25014494]; doi: [https://dx.doi.org/10.1021/pr500322d 10.1021/pr500322d]; GPMDB: [http://gpmdb.org/data/keyword/25014494 8].
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#de Keijzer J, de Haas PE, de Ru AH, van Veelen PA, van Soolingen D,  (2014) &quot;Disclosure of selective advantages in the &quot;modern&quot; sublineage of the Mycobacterium tuberculosis Beijing genotype family by quantitative proteomics.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(10):2632&ndash;45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25022876 25022876]; doi: [https://dx.doi.org/10.1074/mcp.M114.038380 10.1074/mcp.M114.038380]; GPMDB: [http://gpmdb.org/data/keyword/25022876 152].
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#Engel E, Viargues P, Mortier M, Taillebourg E, Cout&eacute; Y, Thevenon D, Fauvarque MO,  (2014) &quot;Identifying USPs regulating immune signals in Drosophila: USP2 deubiquitinates Imd and promotes its degradation by interacting with the proteasome.&quot; <i>Cell Commun Signal</i> <b>12</b>:41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25027767 25027767]; doi: [https://dx.doi.org/10.1186/PREACCEPT-1588328929121802 10.1186/PREACCEPT-1588328929121802]; GPMDB: [http://gpmdb.org/data/keyword/25027767 2].
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#Padden J, Megger DA, Bracht T, Reis H, Ahrens M, Kohl M, Eisenacher M, Schlaak JF, Canbay AE, Weber F, Hoffmann AC, Kuhlmann K, Meyer HE, Baba HA, Sitek B,  (2014) &quot;Identification of novel biomarker candidates for the immunohistochemical diagnosis of cholangiocellular carcinoma.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(10):2661&ndash;72; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25034945 25034945]; doi: [https://dx.doi.org/10.1074/mcp.M113.034942 10.1074/mcp.M113.034942]; GPMDB: [http://gpmdb.org/data/keyword/25034945 16].
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#Naba A, Clauser KR, Whittaker CA, Carr SA, Tanabe KK, Hynes RO,  (2014) &quot;Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver.&quot; <i>BMC Cancer</i> <b>14</b>:518; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25037231 25037231]; doi: [https://dx.doi.org/10.1186/1471-2407-14-518 10.1186/1471-2407-14-518]; GPMDB: [http://gpmdb.org/data/keyword/25037231 176].
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#Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS,  (2014) &quot;In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR).&quot; <i>Mol Cell Proteomics</i> <b>13</b>(11):3152&ndash;63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25038066 25038066]; doi: [https://dx.doi.org/10.1074/mcp.M114.038554 10.1074/mcp.M114.038554]; GPMDB: [http://gpmdb.org/data/keyword/25038066 88].
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#Chen YJ, Ching WC, Chen JS, Lee TY, Lu CT, Chou HC, Lin PY, Khoo KH, Chen JH, Chen YJ,  (2014) &quot;Decoding the s-nitrosoproteomic atlas in individualized human colorectal cancer tissues using a label-free quantitation strategy.&quot; <i>J Proteome Res</i> <b>13</b>(11):4942&ndash;58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25040305 25040305]; doi: [https://dx.doi.org/10.1021/pr5002675 10.1021/pr5002675]; GPMDB: [http://gpmdb.org/data/keyword/25040305 54].
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#Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, NCI CPTAC,  (2014) &quot;Proteogenomic characterization of human colon and rectal cancer.&quot; <i>Nature</i> <b>513</b>(7518):382&ndash;7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25043054 25043054]; doi: [https://dx.doi.org/10.1038/nature13438 10.1038/nature13438]; GPMDB: [http://gpmdb.org/data/keyword/25043054 1381].
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#An E, Narayanan M, Manes NP, Nita-Lazar A,  (2014) &quot;Characterization of functional reprogramming during osteoclast development using quantitative proteomics and mRNA profiling.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(10):2687&ndash;704; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044017 25044017]; doi: [https://dx.doi.org/10.1074/mcp.M113.034371 10.1074/mcp.M113.034371]; GPMDB: [http://gpmdb.org/data/keyword/25044017 73].
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#V&eacute;gh MJ, Rausell A, Loos M, Heldring CM, Jurkowski W, van Nierop P, Paliukhovich I, Li KW, del Sol A, Smit AB, Spijker S, van Kesteren RE,  (2014) &quot;Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(11):2975&ndash;85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044018 25044018]; doi: [https://dx.doi.org/10.1074/mcp.M113.032086 10.1074/mcp.M113.032086]; GPMDB: [http://gpmdb.org/data/keyword/25044018 8].
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#Heo S, Spoerk S, Birner-Gruenberger R, Lubec G,  (2014) &quot;Gel-based mass spectrometric analysis of hippocampal transmembrane proteins using high resolution LTQ Orbitrap Velos Pro.&quot; <i>Proteomics</i> <b>14</b>(17-18):2084&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044505 25044505]; doi: [https://dx.doi.org/10.1002/pmic.201400077 10.1002/pmic.201400077]; GPMDB: [http://gpmdb.org/data/keyword/25044505 60].
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#Aaseb&oslash; E, Vaudel M, Mjaavatten O, Gausdal G, Van der Burgh A, Gjertsen BT, D&oslash;skeland SO, Bruserud O, Berven FS, Selheim F,  (2014) &quot;Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines.&quot; <i>Proteomics</i> <b>14</b>(17-18):1971&ndash;6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044641 25044641]; doi: [https://dx.doi.org/10.1002/pmic.201300448 10.1002/pmic.201300448]; GPMDB: [http://gpmdb.org/data/keyword/25044641 186].
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#Soleilhavoup C, Tsikis G, Labas V, Harichaux G, Kohnke PL, Dacheux JL, Gu&eacute;rin Y, Gatti JL, de Graaf SP, Druart X,  (2014) &quot;Ram seminal plasma proteome and its impact on liquid preservation of spermatozoa.&quot; <i>J Proteomics</i> <b>109</b>:245&ndash;60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25053255 25053255]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.07.007 10.1016/j.jprot.2014.07.007]; GPMDB: [http://gpmdb.org/data/keyword/25053255 114].
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#Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra GJ, Vermeulen M,  (2014) &quot;Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.&quot; <i>Nucleic Acids Res</i> <b>42</b>(15):9880&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25056316 25056316]; doi: [https://dx.doi.org/10.1093/nar/gku661 10.1093/nar/gku661]; GPMDB: [http://gpmdb.org/data/keyword/25056316 62].
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#Tao D, Ubaida-Mohien C, Mathias DK, King JG, Pastrana-Mena R, Tripathi A, Goldowitz I, Graham DR, Moss E, Marti M, Dinglasan RR,  (2014) &quot;Sex-partitioning of the Plasmodium falciparum stage V gametocyte proteome provides insight into falciparum-specific cell biology.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(10):2705&ndash;24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25056935 25056935]; doi: [https://dx.doi.org/10.1074/mcp.M114.040956 10.1074/mcp.M114.040956]; GPMDB: [http://gpmdb.org/data/keyword/25056935 10].
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#Klaubauf S, Narang HM, Post H, Zhou M, Brunner K, Mach-Aigner AR, Mach RL, Heck AJ, Altelaar AF, de Vries RP,  (2014) &quot;Similar is not the same: differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi.&quot; <i>Fungal Genet Biol</i> <b>72</b>:73&ndash;81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25064064 25064064]; doi: [https://dx.doi.org/10.1016/j.fgb.2014.07.007 10.1016/j.fgb.2014.07.007]; GPMDB: [http://gpmdb.org/data/keyword/25064064 40].
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#Putker M, Vos HR, van Dorenmalen K, de Ruiter H, Duran AG, Snel B, Burgering BM, Vermeulen M, Dansen TB,  (2015) &quot;Evolutionary acquisition of cysteines determines FOXO paralog-specific redox signaling.&quot; <i>Antioxid Redox Signal</i> <b>22</b>(1):15&ndash;28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25069953 25069953]; doi: [https://dx.doi.org/10.1089/ars.2014.6056 10.1089/ars.2014.6056]; GPMDB: [http://gpmdb.org/data/keyword/25069953 41].
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#Dephoure N, Hwang S, O&#39;Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM,  (2014) &quot;Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast.&quot; <i>Elife</i> <b>3</b>:e03023; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25073701 25073701]; doi: [https://dx.doi.org/10.7554/eLife.03023 10.7554/eLife.03023]; GPMDB: [http://gpmdb.org/data/keyword/25073701 10].
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#Yang W, Ramachandran A, You S, Jeong H, Morley S, Mulone MD, Logvinenko T, Kim J, Hwang D, Freeman MR, Adam RM,  (2014) &quot;Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells.&quot; <i>Cell Commun Signal</i> <b>12</b>:44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25080971 25080971]; doi: [https://dx.doi.org/10.1186/s12964-014-0044-z 10.1186/s12964-014-0044-z]; GPMDB: [http://gpmdb.org/data/keyword/25080971 30].
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#Labas V, Grasseau I, Cahier K, Gargaros A, Harichaux G, Teixeira-Gomes AP, Alves S, Bourin M, G&eacute;rard N, Blesbois E,  (2015) &quot;Qualitative and quantitative peptidomic and proteomic approaches to phenotyping chicken semen.&quot; <i>J Proteomics</i> <b>112</b>:313&ndash;35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25086240 25086240]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.07.024 10.1016/j.jprot.2014.07.024]; GPMDB: [http://gpmdb.org/data/keyword/25086240 44].
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#Alqahtani A, Heesom K, Bramson JL, Curiel D, Ugai H, Matthews DA,  (2014) &quot;Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics.&quot; <i>J Gen Virol</i> <b>95</b>(Pt 11):2504&ndash;11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096814 25096814]; doi: [https://dx.doi.org/10.1099/vir.0.068221-0 10.1099/vir.0.068221-0]; GPMDB: [http://gpmdb.org/data/keyword/25096814 22].
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#Zhang B, Pirmoradian M, Chernobrovkin A, Zubarev RA,  (2014) &quot;DeMix workflow for efficient identification of cofragmented peptides in high resolution data-dependent tandem mass spectrometry.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(11):3211&ndash;23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25100859 25100859]; doi: [https://dx.doi.org/10.1074/mcp.O114.038877 10.1074/mcp.O114.038877]; GPMDB: [http://gpmdb.org/data/keyword/25100859 7].
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#Wallin MT, Oh U, Nyalwidhe J, Semmes J, Kislinger T, Coffman P, Kurtzke JF, Jacobson S,  (2015) &quot;Serum proteomic analysis of a pre-symptomatic multiple sclerosis cohort.&quot; <i>Eur J Neurol</i> <b>22</b>(3):591&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25104396 25104396]; doi: [https://dx.doi.org/10.1111/ene.12534 10.1111/ene.12534]; GPMDB: [http://gpmdb.org/data/keyword/25104396 104].
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#Perdomo D, A&iuml;t-Ammar N, Syan S, Sachse M, Jhingan GD, Guill&eacute;n N,  (2015) &quot;Cellular and proteomics analysis of the endomembrane system from the unicellular Entamoeba histolytica.&quot; <i>J Proteomics</i> <b>112</b>:125&ndash;40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25109464 25109464]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.07.034 10.1016/j.jprot.2014.07.034]; GPMDB: [http://gpmdb.org/data/keyword/25109464 3].
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#Talman AM, Prieto JH, Marques S, Ubaida-Mohien C, Lawniczak M, Wass MN, Xu T, Frank R, Ecker A, Stanway RS, Krishna S, Sternberg MJ, Christophides GK, Graham DR, Dinglasan RR, Yates JR 3rd, Sinden RE,  (2014) &quot;Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.&quot; <i>Malar J</i> <b>13</b>:315; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25124718 25124718]; doi: [https://dx.doi.org/10.1186/1475-2875-13-315 10.1186/1475-2875-13-315]; GPMDB: [http://gpmdb.org/data/keyword/25124718 3].
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#Carvalho AS, Ribeiro H, Voabil P, Penque D, Jensen ON, Molina H, Matthiesen R,  (2014) &quot;Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(12):3294&ndash;307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25128556 25128556]; doi: [https://dx.doi.org/10.1074/mcp.M113.034363 10.1074/mcp.M113.034363]; GPMDB: [http://gpmdb.org/data/keyword/25128556 18].
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#Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D, Kusebauch U, Moritz RL, Wollscheid B, Lalk M, V&ouml;lker U, Schmidt F,  (2014) &quot;Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells.&quot; <i>Front Microbiol</i> <b>5</b>:392; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25136337 25136337]; doi: [https://dx.doi.org/10.3389/fmicb.2014.00392 10.3389/fmicb.2014.00392]; GPMDB: [http://gpmdb.org/data/keyword/25136337 71].
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#Moczulska KE, Pichler P, Schutzbier M, Schleiffer A, Rumpel S, Mechtler K,  (2014) &quot;Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation.&quot; <i>J Proteome Res</i> <b>13</b>(10):4310&ndash;24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25157418 25157418]; doi: [https://dx.doi.org/10.1021/pr500456t 10.1021/pr500456t]; GPMDB: [http://gpmdb.org/data/keyword/25157418 100].
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#Boj SF, Hwang CI, Baker LA, Chio II, Engle DD, Corbo V, Jager M, Ponz-Sarvise M, Tiriac H, Spector MS, Gracanin A, Oni T, Yu KH, van Boxtel R, Huch M, Rivera KD, Wilson JP, Feigin ME, &Ouml;hlund D, Handly-Santana A, Ardito-Abraham CM, Ludwig M, Elyada E, Alagesan B, Biffi G, Yordanov GN, Delcuze B, Creighton B, Wright K, Park Y, Morsink FH, Molenaar IQ, Borel Rinkes IH, Cuppen E, Hao Y, Jin Y, Nijman IJ, Iacobuzio-Donahue C, Leach SD, Pappin DJ, Hammell M, Klimstra DS, Basturk O, Hruban RH, Offerhaus GJ, Vries RG, Clevers H, Tuveson DA,  (2015) &quot;Organoid models of human and mouse ductal pancreatic cancer.&quot; <i>Cell</i> <b>160</b>(1-2):324&ndash;38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25557080 25557080]; doi: [https://dx.doi.org/10.1016/j.cell.2014.12.021 10.1016/j.cell.2014.12.021]; GPMDB: [http://gpmdb.org/data/keyword/25557080 4].
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#Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R,  (2015) &quot;Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(3):739&ndash;49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25561506 25561506]; doi: [https://dx.doi.org/10.1074/mcp.M113.035550 10.1074/mcp.M113.035550]; GPMDB: [http://gpmdb.org/data/keyword/25561506 46].
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#Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM,  (2015) &quot;The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response.&quot; <i>PLoS Genet</i> <b>11</b>(1):e1004903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25569619 25569619]; doi: [https://dx.doi.org/10.1371/journal.pgen.1004903 10.1371/journal.pgen.1004903]; GPMDB: [http://gpmdb.org/data/keyword/25569619 20].
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#Zappacosta F, Scott GF, Huddleston MJ, Annan RS,  (2015) &quot;An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome.&quot; <i>J Proteome Res</i> <b>14</b>(2):997&ndash;1009; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25575281 25575281]; doi: [https://dx.doi.org/10.1021/pr501025e 10.1021/pr501025e]; GPMDB: [http://gpmdb.org/data/keyword/25575281 42].
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#Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M,  (2015) &quot;Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(3):658&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25576301 25576301]; doi: [https://dx.doi.org/10.1074/mcp.M114.042812 10.1074/mcp.M114.042812]; GPMDB: [http://gpmdb.org/data/keyword/25576301 40].
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#Chiang DY, Lebesgue N, Beavers DL, Alsina KM, Damen JM, Voigt N, Dobrev D, Wehrens XH, Scholten A,  (2015) &quot;Alterations in the interactome of serine/threonine protein phosphatase type-1 in atrial fibrillation patients.&quot; <i>J Am Coll Cardiol</i> <b>65</b>(2):163&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25593058 25593058]; doi: [https://dx.doi.org/10.1016/j.jacc.2014.10.042 10.1016/j.jacc.2014.10.042]; GPMDB: [http://gpmdb.org/data/keyword/25593058 22].
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#Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma &Uuml;, K&otilde;ks S, Salumets A,  (2015) &quot;Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment.&quot; <i>Proteomics</i> <b>15</b>(11):1906&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25603787 25603787]; doi: [https://dx.doi.org/10.1002/pmic.201400297 10.1002/pmic.201400297]; GPMDB: [http://gpmdb.org/data/keyword/25603787 16].
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#Byron A, Askari JA, Humphries JD, Jacquemet G, Koper EJ, Warwood S, Choi CK, Stroud MJ, Chen CS, Knight D, Humphries MJ,  (2015) &quot;A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting.&quot; <i>Nat Commun</i> <b>6</b>:6135; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25609142 25609142]; doi: [https://dx.doi.org/10.1038/ncomms7135 10.1038/ncomms7135]; GPMDB: [http://gpmdb.org/data/keyword/25609142 237].
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#Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M,  (2015) &quot;Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(4):841&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25616865 25616865]; doi: [https://dx.doi.org/10.1074/mcp.M114.044222 10.1074/mcp.M114.044222]; GPMDB: [http://gpmdb.org/data/keyword/25616865 6].
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#Ramond E, Gesbert G, Guerrera IC, Chhuon C, Dupuis M, Rigard M, Henry T, Barel M, Charbit A,  (2015) &quot;Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(4):870&ndash;81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25616868 25616868]; doi: [https://dx.doi.org/10.1074/mcp.M114.044552 10.1074/mcp.M114.044552]; GPMDB: [http://gpmdb.org/data/keyword/25616868 18].
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#Loroch S, Schommartz T, Brune W, Zahedi RP, Sickmann A,  (2015) &quot;Multidimensional electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedical research.&quot; <i>Biochim Biophys Acta</i> <b>1854</b>(5):460&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25619855 25619855]; doi: [https://dx.doi.org/10.1016/j.bbapap.2015.01.006 10.1016/j.bbapap.2015.01.006]; GPMDB: [http://gpmdb.org/data/keyword/25619855 36].
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#Harel M, Oren-Giladi P, Kaidar-Person O, Shaked Y, Geiger T,  (2015) &quot;Proteomics of microparticles with SILAC Quantification (PROMIS-Quan): a novel proteomic method for plasma biomarker quantification.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(4):1127&ndash;36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25624350 25624350]; doi: [https://dx.doi.org/10.1074/mcp.M114.043364 10.1074/mcp.M114.043364]; GPMDB: [http://gpmdb.org/data/keyword/25624350 46].
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#Zanker D, Otto W, Chen W, von Bergen M, Tomm JM,  (2015) &quot;Compartment resolved reference proteome map from highly purified na&iuml;ve, activated, effector, and memory CD8&#x207A; murine immune cells.&quot; <i>Proteomics</i> <b>15</b>(11):1808&ndash;12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643623 25643623]; doi: [https://dx.doi.org/10.1002/pmic.201400405 10.1002/pmic.201400405]; GPMDB: [http://gpmdb.org/data/keyword/25643623 249].
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#Murgia M, Nagaraj N, Deshmukh AS, Zeiler M, Cancellara P, Moretti I, Reggiani C, Schiaffino S, Mann M,  (2015) &quot;Single muscle fiber proteomics reveals unexpected mitochondrial specialization.&quot; <i>EMBO Rep</i> <b>16</b>(3):387&ndash;95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643707 25643707]; doi: [https://dx.doi.org/10.15252/embr.201439757 10.15252/embr.201439757]; GPMDB: [http://gpmdb.org/data/keyword/25643707 89].
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#Marza E, Taouji S, Barroso K, Raymond AA, Guignard L, Bonneu M, Pallares-Lupon N, Dupuy JW, Fernandez-Zapico ME, Rosenbaum J, Palladino F, Dupuy D, Chevet E,  (2015) &quot;Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription.&quot; <i>EMBO Rep</i> <b>16</b>(3):332&ndash;40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25652260 25652260]; doi: [https://dx.doi.org/10.15252/embr.201439123 10.15252/embr.201439123]; GPMDB: [http://gpmdb.org/data/keyword/25652260 6].
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#Corradini E, Burgers PP, Plank M, Heck AJ, Scholten A,  (2015) &quot;Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase I&beta; isoform.&quot; <i>J Biol Chem</i> <b>290</b>(12):7887&ndash;96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25653285 25653285]; doi: [https://dx.doi.org/10.1074/jbc.M114.622613 10.1074/jbc.M114.622613]; GPMDB: [http://gpmdb.org/data/keyword/25653285 6].
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#Sandin M, Chawade A, Levander F,  (2015) &quot;Is label-free LC-MS/MS ready for biomarker discovery?&quot; <i>Proteomics Clin Appl</i> <b>9</b>(3-4):289&ndash;94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25656266 25656266]; doi: [https://dx.doi.org/10.1002/prca.201400202 10.1002/prca.201400202]; GPMDB: [http://gpmdb.org/data/keyword/25656266 2].
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#Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC,  (2015) &quot;Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(4):961&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660013 25660013]; doi: [https://dx.doi.org/10.1074/mcp.M114.045260 10.1074/mcp.M114.045260]; GPMDB: [http://gpmdb.org/data/keyword/25660013 60].
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#M&eacute;dard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B,  (2015) &quot;Optimized chemical proteomics assay for kinase inhibitor profiling.&quot; <i>J Proteome Res</i> <b>14</b>(3):1574&ndash;86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660469 25660469]; doi: [https://dx.doi.org/10.1021/pr5012608 10.1021/pr5012608]; GPMDB: [http://gpmdb.org/data/keyword/25660469 126].
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#Diner BA, Li T, Greco TM, Crow MS, Fuesler JA, Wang J, Cristea IM,  (2015) &quot;The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA.&quot; <i>Mol Syst Biol</i> <b>11</b>(1):787; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25665578 25665578]; GPMDB: [http://gpmdb.org/data/keyword/25665578 21].
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#Jacques S, Ghesqui&egrave;re B, De Bock PJ, Demol H, Wahni K, Willems P, Messens J, Van Breusegem F, Gevaert K,  (2015) &quot;Protein Methionine Sulfoxide Dynamics in Arabidopsis thaliana under Oxidative Stress.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(5):1217&ndash;29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25693801 25693801]; doi: [https://dx.doi.org/10.1074/mcp.M114.043729 10.1074/mcp.M114.043729]; GPMDB: [http://gpmdb.org/data/keyword/25693801 2].
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#Hu J, Huang X, Chen L, Sun X, Lu C, Zhang L, Wang Y, Zuo J,  (2015) &quot;Site-specific nitrosoproteomic identification of endogenously S-nitrosylated proteins in Arabidopsis.&quot; <i>Plant Physiol</i> <b>167</b>(4):1731&ndash;46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25699590 25699590]; doi: [https://dx.doi.org/10.1104/pp.15.00026 10.1104/pp.15.00026]; GPMDB: [http://gpmdb.org/data/keyword/25699590 12].
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#Peebo K, Valgepea K, Maser A, Nahku R, Adamberg K, Vilu R,  (2015) &quot;Proteome reallocation in Escherichia coli with increasing specific growth rate.&quot; <i>Mol Biosyst</i> <b>11</b>(4):1184&ndash;93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25712329 25712329]; doi: [https://dx.doi.org/10.1039/c4mb00721b 10.1039/c4mb00721b]; GPMDB: [http://gpmdb.org/data/keyword/25712329 26].
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#Koganti S, Clark C, Zhi J, Li X, Chen EI, Chakrabortty S, Hill ER, Bhaduri-McIntosh S,  (2015) &quot;Cellular STAT3 functions via PCBP2 to restrain Epstein-Barr Virus lytic activation in B lymphocytes.&quot; <i>J Virol</i> <b>89</b>(9):5002&ndash;11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25717101 25717101]; doi: [https://dx.doi.org/10.1128/JVI.00121-15 10.1128/JVI.00121-15]; GPMDB: [http://gpmdb.org/data/keyword/25717101 2].
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#Kettenbach AN, Deng L, Wu Y, Baldissard S, Adamo ME, Gerber SA, Moseley JB,  (2015) &quot;Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(5):1275&ndash;87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25720772 25720772]; doi: [https://dx.doi.org/10.1074/mcp.M114.045245 10.1074/mcp.M114.045245]; GPMDB: [http://gpmdb.org/data/keyword/25720772 96].
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#Gonz&aacute;lez-Prieto R, Cuijpers SA, Luijsterburg MS, van Attikum H, Vertegaal AC,  (2015) &quot;SUMOylation and PARylation cooperate to recruit and stabilize SLX4 at DNA damage sites.&quot; <i>EMBO Rep</i> <b>16</b>(4):512&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25722289 25722289]; doi: [https://dx.doi.org/10.15252/embr.201440017 10.15252/embr.201440017]; GPMDB: [http://gpmdb.org/data/keyword/25722289 27].
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#Keshishian H, Burgess MW, Gillette MA, Mertins P, Clauser KR, Mani DR, Kuhn EW, Farrell LA, Gerszten RE, Carr SA,  (2015) &quot;Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(9):2375&ndash;93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25724909 25724909]; doi: [https://dx.doi.org/10.1074/mcp.M114.046813 10.1074/mcp.M114.046813]; GPMDB: [http://gpmdb.org/data/keyword/25724909 298].
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#Vogel CJ, Smit MA, Maddalo G, Possik PA, Sparidans RW, van der Burg SH, Verdegaal EM, Heck AJ, Samatar AA, Beijnen JH, Altelaar AF, Peeper DS,  (2015) &quot;Cooperative induction of apoptosis in NRAS mutant melanoma by inhibition of MEK and ROCK.&quot; <i>Pigment Cell Melanoma Res</i> <b>28</b>(3):307&ndash;17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25728708 25728708]; doi: [https://dx.doi.org/10.1111/pcmr.12364 10.1111/pcmr.12364]; GPMDB: [http://gpmdb.org/data/keyword/25728708 170].
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#Zhang H, Deery MJ, Gannon L, Powers SJ, Lilley KS, Theodoulou FL,  (2015) &quot;Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots.&quot; <i>Proteomics</i> <b>15</b>(14):2447&ndash;57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25728785 25728785]; doi: [https://dx.doi.org/10.1002/pmic.201400530 10.1002/pmic.201400530]; GPMDB: [http://gpmdb.org/data/keyword/25728785 14].
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#Aller K, Adamberg K, Reile I, Timarova V, Peebo K, Vilu R,  (2015) &quot;Excess of threonine compared with serine promotes threonine aldolase activity in Lactococcus lactis IL1403.&quot; <i>Microbiology</i> <b>161</b>(Pt 5):1073&ndash;80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25743155 25743155]; doi: [https://dx.doi.org/10.1099/mic.0.000071 10.1099/mic.0.000071]; GPMDB: [http://gpmdb.org/data/keyword/25743155 6].
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#&Scaron;talekar M, Yin X, Rebolj K, Darovic S, Troakes C, Mayr M, Shaw CE, Rogelj B,  (2015) &quot;Proteomic analyses reveal that loss of TDP-43 affects RNA processing and intracellular transport.&quot; <i>Neuroscience</i> <b>293</b>:157&ndash;70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25743254 25743254]; doi: [https://dx.doi.org/10.1016/j.neuroscience.2015.02.046 10.1016/j.neuroscience.2015.02.046]; GPMDB: [http://gpmdb.org/data/keyword/25743254 96].
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#Jamdhade MD, Pawar H, Chavan S, Sathe G, Umasankar PK, Mahale KN, Dixit T, Madugundu AK, Prasad TS, Gowda H, Pandey A, Patole MS,  (2015) &quot;Comprehensive proteomics analysis of glycosomes from Leishmania donovani.&quot; <i>OMICS</i> <b>19</b>(3):157&ndash;70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25748437 25748437]; doi: [https://dx.doi.org/10.1089/omi.2014.0163 10.1089/omi.2014.0163]; GPMDB: [http://gpmdb.org/data/keyword/25748437 2].
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#Willger SD, Liu Z, Olarte RA, Adamo ME, Stajich JE, Myers LC, Kettenbach AN, Hogan DA,  (2015) &quot;Analysis of the Candida albicans Phosphoproteome.&quot; <i>Eukaryot Cell</i> <b>14</b>(5):474&ndash;85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25750214 25750214]; doi: [https://dx.doi.org/10.1128/EC.00011-15 10.1128/EC.00011-15]; GPMDB: [http://gpmdb.org/data/keyword/25750214 13].
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#Sch&ouml;lz C, Weinert BT, Wagner SA, Beli P, Miyake Y, Qi J, Jensen LJ, Streicher W, McCarthy AR, Westwood NJ, Lain S, Cox J, Matthias P, Mann M, Bradner JE, Choudhary C,  (2015) &quot;Acetylation site specificities of lysine deacetylase inhibitors in human cells.&quot; <i>Nat Biotechnol</i> <b>33</b>(4):415&ndash;23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25751058 25751058]; doi: [https://dx.doi.org/10.1038/nbt.3130 10.1038/nbt.3130]; GPMDB: [http://gpmdb.org/data/keyword/25751058 292].
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#Alvarez Hayes J, Lamberti Y, Surmann K, Schmidt F, V&ouml;lker U, Rodriguez ME,  (2015) &quot;Shotgun proteome analysis of Bordetella pertussis reveals a distinct influence of iron availability on the bacterial metabolism, virulence, and defense response.&quot; <i>Proteomics</i> <b>15</b>(13):2258&ndash;66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25755163 25755163]; doi: [https://dx.doi.org/10.1002/pmic.201400512 10.1002/pmic.201400512]; GPMDB: [http://gpmdb.org/data/keyword/25755163 6].
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#Xiao Z, Chang JG, Hendriks IA, Sigur&eth;sson JO, Olsen JV, Vertegaal AC,  (2015) &quot;System-wide Analysis of SUMOylation Dynamics in Response to Replication Stress Reveals Novel Small Ubiquitin-like Modified Target Proteins and Acceptor Lysines Relevant for Genome Stability.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(5):1419&ndash;34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25755297 25755297]; doi: [https://dx.doi.org/10.1074/mcp.O114.044792 10.1074/mcp.O114.044792]; GPMDB: [http://gpmdb.org/data/keyword/25755297 84].
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#Dill BD, Gierlinski M, H&auml;rtlova A, Arandilla AG, Guo M, Clarke RG, Trost M,  (2015) &quot;Quantitative proteome analysis of temporally resolved phagosomes following uptake via key phagocytic receptors.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(5):1334&ndash;49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25755298 25755298]; doi: [https://dx.doi.org/10.1074/mcp.M114.044594 10.1074/mcp.M114.044594]; GPMDB: [http://gpmdb.org/data/keyword/25755298 91].
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#Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M,  (2015) &quot;Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).&quot; <i>Mol Cell Proteomics</i> <b>14</b>(5):1350&ndash;60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25755299 25755299]; doi: [https://dx.doi.org/10.1074/mcp.M114.042499 10.1074/mcp.M114.042499]; GPMDB: [http://gpmdb.org/data/keyword/25755299 96].
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#Carter DM, Westdorp K, Noon KR, Terhune SS,  (2015) &quot;Proteomic identification of nuclear processes manipulated by cytomegalovirus early during infection.&quot; <i>Proteomics</i> <b>15</b>(12):1995&ndash;2005; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25758553 25758553]; doi: [https://dx.doi.org/10.1002/pmic.201400599 10.1002/pmic.201400599]; GPMDB: [http://gpmdb.org/data/keyword/25758553 8].
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#Martin-Perez M, Vill&eacute;n J,  (2015) &quot;Feasibility of protein turnover studies in prototroph Saccharomyces cerevisiae strains.&quot; <i>Anal Chem</i> <b>87</b>(7):4008&ndash;14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25767917 25767917]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b00264 10.1021/acs.analchem.5b00264]; GPMDB: [http://gpmdb.org/data/keyword/25767917 22].
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#Zub KA, Sousa MM, Sarno A, Sharma A, Demirovic A, Rao S, Young C, Aas PA, Ericsson I, Sundan A, Jensen ON, Slupphaug G,  (2015) &quot;Modulation of cell metabolic pathways and oxidative stress signaling contribute to acquired melphalan resistance in multiple myeloma cells.&quot; <i>PLoS One</i> <b>10</b>(3):e0119857; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25769101 25769101]; doi: [https://dx.doi.org/10.1371/journal.pone.0119857 10.1371/journal.pone.0119857]; GPMDB: [http://gpmdb.org/data/keyword/25769101 12].
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#Hoover H, Li J, Marchese J, Rothwell C, Borawoski J, Jeffery DA, Gaither LA, Finkel N,  (2015) &quot;Quantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers.&quot; <i>J Proteome Res</i> <b>14</b>(9):3670&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26151158 26151158]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00508 10.1021/acs.jproteome.5b00508]; GPMDB: [http://gpmdb.org/data/keyword/26151158 27].
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#Huber RJ, O&#39;Day DH,  (2015) &quot;Proteomic profiling of the extracellular matrix (slime sheath) of Dictyostelium discoideum.&quot; <i>Proteomics</i> <b>15</b>(19):3315&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26152465 26152465]; doi: [https://dx.doi.org/10.1002/pmic.201500143 10.1002/pmic.201500143]; GPMDB: [http://gpmdb.org/data/keyword/26152465 23].
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#Moche M, Schl&uuml;ter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D,  (2015) &quot;Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions.&quot; <i>J Proteome Res</i> <b>14</b>(9):3804&ndash;22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26152824 26152824]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00148 10.1021/acs.jproteome.5b00148]; GPMDB: [http://gpmdb.org/data/keyword/26152824 924].
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#Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alp&iacute;zar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R,  (2015) &quot;An open-source computational and data resource to analyze digital maps of immunopeptidomes.&quot; <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26154972 26154972]; doi: [https://dx.doi.org/10.7554/eLife.07661 10.7554/eLife.07661]; GPMDB: [http://gpmdb.org/data/keyword/26154972 70].
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#Jumeau F, Com E, Lane L, Duek P, Lagarrigue M, Lavigne R, Guillot L, Rondel K, Gateau A, Melaine N, Gu&eacute;vel B, Sergeant N, Mitchell V, Pineau C,  (2015) &quot;Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project.&quot; <i>J Proteome Res</i> <b>14</b>(9):3606&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26168773 26168773]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00170 10.1021/acs.jproteome.5b00170]; GPMDB: [http://gpmdb.org/data/keyword/26168773 63].
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#Schiller HB, Fernandez IE, Burgstaller G, Schaab C, Scheltema RA, Schwarzmayr T, Strom TM, Eickelberg O, Mann M,  (2015) &quot;Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair.&quot; <i>Mol Syst Biol</i> <b>11</b>(7):819; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26174933 26174933]; GPMDB: [http://gpmdb.org/data/keyword/26174933 228].
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#Morley S, You S, Pollan S, Choi J, Zhou B, Hager MH, Steadman K, Spinelli C, Rajendran K, Gertych A, Kim J, Adam RM, Yang W, Krishnan R, Knudsen BS, Di Vizio D, Freeman MR,  (2015) &quot;Regulation of microtubule dynamics by DIAPH3 influences amoeboid tumor cell mechanics and sensitivity to taxanes.&quot; <i>Sci Rep</i> <b>5</b>:12136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26179371 26179371]; doi: [https://dx.doi.org/10.1038/srep12136 10.1038/srep12136]; GPMDB: [http://gpmdb.org/data/keyword/26179371 16].
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#Feng S, Powell SM, Wilson R, Bowman JP,  (2015) &quot;Proteomic Insight into Functional Changes of Proteorhodopsin-Containing Bacterial Species Psychroflexus torquis under Different Illumination and Salinity Levels.&quot; <i>J Proteome Res</i> <b>14</b>(9):3848&ndash;58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26179671 26179671]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00241 10.1021/acs.jproteome.5b00241]; GPMDB: [http://gpmdb.org/data/keyword/26179671 72].
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#Selvan LD, Sreenivasamurthy SK, Kumar S, Yelamanchi SD, Madugundu AK, Anil AK, Renuse S, Nair BG, Gowda H, Mathur PP, Satishchandra P, Shankar SK, Mahadevan A, Keshava Prasad TS,  (2015) &quot;Characterization of host response to Cryptococcus neoformans through quantitative proteomic analysis of cryptococcal meningitis co-infected with HIV.&quot; <i>Mol Biosyst</i> <b>11</b>(9):2529&ndash;40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26181685 26181685]; doi: [https://dx.doi.org/10.1039/c5mb00187k 10.1039/c5mb00187k]; GPMDB: [http://gpmdb.org/data/keyword/26181685 1].
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#H&uuml;nten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, Zimmer R, Warscheid B, Hermeking H,  (2015) &quot;p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(10):2609&ndash;29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26183718 26183718]; doi: [https://dx.doi.org/10.1074/mcp.M115.050237 10.1074/mcp.M115.050237]; GPMDB: [http://gpmdb.org/data/keyword/26183718 120].
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#Bish R, Cuevas-Polo N, Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C,  (2015) &quot;Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins.&quot; <i>Biomolecules</i> <b>5</b>(3):1441&ndash;66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26184334 26184334]; doi: [https://dx.doi.org/10.3390/biom5031441 10.3390/biom5031441]; GPMDB: [http://gpmdb.org/data/keyword/26184334 50].
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#Nystr&ouml;m A, Thriene K, Mittapalli V, Kern JS, Kiritsi D, Dengjel J, Bruckner-Tuderman L,  (2015) &quot;Losartan ameliorates dystrophic epidermolysis bullosa and uncovers new disease mechanisms.&quot; <i>EMBO Mol Med</i> <b>7</b>(9):1211&ndash;28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26194911 26194911]; doi: [https://dx.doi.org/10.15252/emmm.201505061 10.15252/emmm.201505061]; GPMDB: [http://gpmdb.org/data/keyword/26194911 110].
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#Zheng B, Zhao D, Zhang P, Shen C, Guo Y, Zhou T, Guo X, Zhou Z, Sha J,  (2015) &quot;Quantitative Proteomics Reveals the Essential Roles of Stromal Interaction Molecule 1 (STIM1) in the Testicular Cord Formation in Mouse Testis.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(10):2682&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26199344 26199344]; doi: [https://dx.doi.org/10.1074/mcp.M115.049569 10.1074/mcp.M115.049569]; GPMDB: [http://gpmdb.org/data/keyword/26199344 2].
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#Wang IX, Ramrattan G, Cheung VG,  (2015) &quot;Genetic variation in insulin-induced kinase signaling.&quot; <i>Mol Syst Biol</i> <b>11</b>(7):820; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26202599 26202599]; GPMDB: [http://gpmdb.org/data/keyword/26202599 46].
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#Corradini E, Klaasse G, Leurs U, Heck AJ, Martin NI, Scholten A,  (2015) &quot;Charting the interactome of PDE3A in human cells using an IBMX based chemical proteomics approach.&quot; <i>Mol Biosyst</i> <b>11</b>(10):2786&ndash;97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26205238 26205238]; doi: [https://dx.doi.org/10.1039/c5mb00142k 10.1039/c5mb00142k]; GPMDB: [http://gpmdb.org/data/keyword/26205238 47].
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#Courtney DG, Poulsen ET, Kennedy S, Moore JE, Atkinson SD, Maurizi E, Nesbit MA, Moore CB, Enghild JJ,  (2015) &quot;Protein Composition of TGFBI-R124C- and TGFBI-R555W-Associated Aggregates Suggests Multiple Mechanisms Leading to Lattice and Granular Corneal Dystrophy.&quot; <i>Invest Ophthalmol Vis Sci</i> <b>56</b>(8):4653&ndash;61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26207300 26207300]; doi: [https://dx.doi.org/10.1167/iovs.15-16922 10.1167/iovs.15-16922]; GPMDB: [http://gpmdb.org/data/keyword/26207300 39].
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#D&iacute;ez P, Droste C, D&eacute;gano RM, Gonz&aacute;lez-Mu&ntilde;oz M, Ibarrola N, P&eacute;rez-Andr&eacute;s M, Garin-Muga A, Segura V, Marko-Varga G, LaBaer J, Orfao A, Corrales FJ, De Las Rivas J, Fuentes M,  (2015) &quot;Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project.&quot; <i>J Proteome Res</i> <b>14</b>(9):3530&ndash;40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26216070 26216070]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00474 10.1021/acs.jproteome.5b00474]; GPMDB: [http://gpmdb.org/data/keyword/26216070 60].
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#Berger ST, Ahmed S, Muntel J, Cuevas Polo N, Bachur R, Kentsis A, Steen J, Steen H,  (2015) &quot;MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(10):2814&ndash;23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26223766 26223766]; doi: [https://dx.doi.org/10.1074/mcp.O115.049650 10.1074/mcp.O115.049650]; GPMDB: [http://gpmdb.org/data/keyword/26223766 113].
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#Woo J, Han D, Park J, Kim SJ, Kim Y,  (2015) &quot;In-depth characterization of the secretome of mouse CNS cell lines by LC-MS/MS without prefractionation.&quot; <i>Proteomics</i> <b>15</b>(21):3617&ndash;22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26227174 26227174]; doi: [https://dx.doi.org/10.1002/pmic.201400623 10.1002/pmic.201400623]; GPMDB: [http://gpmdb.org/data/keyword/26227174 27].
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#Guo H, Garcia-Vedrenne AE, Isserlin R, Lugowski A, Morada A, Sun A, Miao Y, Kuzmanov U, Wan C, Ma H, Foltz K, Emili A,  (2015) &quot;Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation.&quot; <i>Proteomics</i> <b>15</b>(23-24):4080&ndash;95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26227301 26227301]; doi: [https://dx.doi.org/10.1002/pmic.201500159 10.1002/pmic.201500159]; GPMDB: [http://gpmdb.org/data/keyword/26227301 182].
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#Na YR, Hong JH, Lee MY, Jung JH, Jung D, Kim YW, Son D, Choi M, Kim KP, Seok SH 2nd,  (2015) &quot;Proteomic Analysis Reveals Distinct Metabolic Differences Between Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF) and Macrophage Colony Stimulating Factor (M-CSF) Grown Macrophages Derived from Murine Bone Marrow Cells.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(10):2722&ndash;32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26229149 26229149]; doi: [https://dx.doi.org/10.1074/mcp.M115.048744 10.1074/mcp.M115.048744]; GPMDB: [http://gpmdb.org/data/keyword/26229149 16].
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#Haurogn&eacute; K, Pavlovic M, Rogniaux H, Bach JM, Lieubeau B,  (2015) &quot;Type 1 Diabetes Prone NOD Mice Have Diminished Cxcr1 mRNA Expression in Polymorphonuclear Neutrophils and CD4+ T Lymphocytes.&quot; <i>PLoS One</i> <b>10</b>(7):e0134365; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26230114 26230114]; doi: [https://dx.doi.org/10.1371/journal.pone.0134365 10.1371/journal.pone.0134365]; GPMDB: [http://gpmdb.org/data/keyword/26230114 12].
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#Subasic D, Br&uuml;mmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Goetze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner MO,  (2015) &quot;Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.&quot; <i>Genome Res</i> <b>25</b>(11):1680&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26232411 26232411]; doi: [https://dx.doi.org/10.1101/gr.183160.114 10.1101/gr.183160.114]; GPMDB: [http://gpmdb.org/data/keyword/26232411 52].
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#Wi&#x15B;niewski JR, Du&#x15B;-Szachniewicz K, Ostasiewicz P, Zi&oacute;&#x142;kowski P, Rakus D, Mann M,  (2015) &quot;Absolute Proteome Analysis of Colorectal Mucosa, Adenoma, and Cancer Reveals Drastic Changes in Fatty Acid Metabolism and Plasma Membrane Transporters.&quot; <i>J Proteome Res</i> <b>14</b>(9):4005&ndash;18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26245529 26245529]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00523 10.1021/acs.jproteome.5b00523]; GPMDB: [http://gpmdb.org/data/keyword/26245529 184].
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#Hou J, Wang X, McShane E, Zauber H, Sun W, Selbach M, Chen W,  (2015) &quot;Extensive allele-specific translational regulation in hybrid mice.&quot; <i>Mol Syst Biol</i> <b>11</b>(8):825; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26253569 26253569]; GPMDB: [http://gpmdb.org/data/keyword/26253569 3].
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#Shah P, Wang X, Yang W, Toghi Eshghi S, Sun S, Hoti N, Chen L, Yang S, Pasay J, Rubin A, Zhang H,  (2015) &quot;Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(10):2753&ndash;63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26256267 26256267]; doi: [https://dx.doi.org/10.1074/mcp.M115.047928 10.1074/mcp.M115.047928]; GPMDB: [http://gpmdb.org/data/keyword/26256267 24].
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#Toledo A, P&eacute;rez A, Coleman JL, Benach JL,  (2015) &quot;The lipid raft proteome of Borrelia burgdorferi.&quot; <i>Proteomics</i> <b>15</b>(21):3662&ndash;75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26256460 26256460]; doi: [https://dx.doi.org/10.1002/pmic.201500093 10.1002/pmic.201500093]; GPMDB: [http://gpmdb.org/data/keyword/26256460 18].
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#Kwon OK, Lee W, Kim SJ, Lee YM, Lee JY, Kim JY, Bae JS, Lee S,  (2015) &quot;In-depth proteomics approach of secretome to identify novel biomarker for sepsis in LPS-stimulated endothelial cells.&quot; <i>Electrophoresis</i> <b>36</b>(23):2851&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26257168 26257168]; doi: [https://dx.doi.org/10.1002/elps.201500198 10.1002/elps.201500198]; GPMDB: [http://gpmdb.org/data/keyword/26257168 4].
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#He P, Zhao L, Zhu L, Weinman EJ, De Giorgio R, Koval M, Srinivasan S, Yun CC,  (2015) &quot;Restoration of Na+/H+ exchanger NHE3-containing macrocomplexes ameliorates diabetes-associated fluid loss.&quot; <i>J Clin Invest</i> <b>125</b>(9):3519&ndash;31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26258413 26258413]; doi: [https://dx.doi.org/10.1172/JCI79552 10.1172/JCI79552]; GPMDB: [http://gpmdb.org/data/keyword/26258413 20].
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#Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan EC, Zhou L,  (2015) &quot;Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress.&quot; <i>J Proteome Res</i> <b>14</b>(9):3982&ndash;95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26260330 26260330]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00443 10.1021/acs.jproteome.5b00443]; GPMDB: [http://gpmdb.org/data/keyword/26260330 3].
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#Dubois L, Ronquist KK, Ek B, Ronquist G, Larsson A,  (2015) &quot;Proteomic Profiling of Detergent Resistant Membranes (Lipid Rafts) of Prostasomes.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(11):3015&ndash;22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26272980 26272980]; doi: [https://dx.doi.org/10.1074/mcp.M114.047530 10.1074/mcp.M114.047530]; GPMDB: [http://gpmdb.org/data/keyword/26272980 1].
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#Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO,  (2015) &quot;Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.&quot; <i>PLoS Comput Biol</i> <b>11</b>(8):e1004400; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26275208 26275208]; doi: [https://dx.doi.org/10.1371/journal.pcbi.1004400 10.1371/journal.pcbi.1004400]; GPMDB: [http://gpmdb.org/data/keyword/26275208 54].
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#Kauko O, Laajala TD, Jumppanen M, Hintsanen P, Suni V, Haapaniemi P, Corthals G, Aittokallio T, Westermarck J, Imanishi SY,  (2015) &quot;Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling.&quot; <i>Sci Rep</i> <b>5</b>:13099; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26278961 26278961]; doi: [https://dx.doi.org/10.1038/srep13099 10.1038/srep13099]; GPMDB: [http://gpmdb.org/data/keyword/26278961 30].
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#Humphrey SJ, Azimifar SB, Mann M,  (2015) &quot;High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics.&quot; <i>Nat Biotechnol</i> <b>33</b>(9):990&ndash;5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26280412 26280412]; doi: [https://dx.doi.org/10.1038/nbt.3327 10.1038/nbt.3327]; GPMDB: [http://gpmdb.org/data/keyword/26280412 199].
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#Zhang Y, Li Q, Wu F, Zhou R, Qi Y, Su N, Chen L, Xu S, Jiang T, Zhang C, Cheng G, Chen X, Kong D, Wang Y, Zhang T, Zi J, Wei W, Gao Y, Zhen B, Xiong Z, Wu S, Yang P, Wang Q, Wen B, He F, Xu P, Liu S,  (2015) &quot;Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins.&quot; <i>J Proteome Res</i> <b>14</b>(9):3583&ndash;94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26282447 26282447]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00435 10.1021/acs.jproteome.5b00435]; GPMDB: [http://gpmdb.org/data/keyword/26282447 150].
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#De Marchi T, Liu NQ, Stingl C, Timmermans MA, Smid M, Look MP, Tjoa M, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Kliffen M, Luider TM, Foekens JA, Martens JW, Umar A,  (2016) &quot;4-protein signature predicting tamoxifen treatment outcome in recurrent breast cancer.&quot; <i>Mol Oncol</i> <b>10</b>(1):24&ndash;39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26285647 26285647]; doi: [https://dx.doi.org/10.1016/j.molonc.2015.07.004 10.1016/j.molonc.2015.07.004]; GPMDB: [http://gpmdb.org/data/keyword/26285647 112].
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#Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast &Aacute;M, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA,  (2015) &quot;Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors.&quot; <i>Cell Stem Cell</i> <b>17</b>(4):422&ndash;34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26299573 26299573]; doi: [https://dx.doi.org/10.1016/j.stem.2015.07.007 10.1016/j.stem.2015.07.007]; GPMDB: [http://gpmdb.org/data/keyword/26299573 240].
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#Titz B, Sewer A, Schneider T, Elamin A, Martin F, Dijon S, Luettich K, Guedj E, Vuillaume G, Ivanov NV, Peck MJ, Chaudhary NI, Hoeng J, Peitsch MC,  (2015) &quot;Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects.&quot; <i>J Proteomics</i> <b>128</b>:306&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26306861 26306861]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.08.009 10.1016/j.jprot.2015.08.009]; GPMDB: [http://gpmdb.org/data/keyword/26306861 120].
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#Yang CR, Raghuram V, Emamian M, Sandoval PC, Knepper MA,  (2015) &quot;Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling.&quot; <i>Am J Physiol Cell Physiol</i> <b>309</b>(12):C799&ndash;812; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26310817 26310817]; doi: [https://dx.doi.org/10.1152/ajpcell.00214.2015 10.1152/ajpcell.00214.2015]; GPMDB: [http://gpmdb.org/data/keyword/26310817 257].
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#Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE,  (2016) &quot;Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases.&quot; <i>Cell Rep</i> <b>14</b>(5):1049&ndash;61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832403 26832403]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.01.009 10.1016/j.celrep.2016.01.009]; GPMDB: [http://gpmdb.org/data/keyword/26832403 486].
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#Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE,  (2016) &quot;miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.&quot; <i>Cancer Cell</i> <b>29</b>(2):214&ndash;28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832662 26832662]; doi: [https://dx.doi.org/10.1016/j.ccell.2015.12.011 10.1016/j.ccell.2015.12.011]; GPMDB: [http://gpmdb.org/data/keyword/26832662 72].
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#Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ,  (2016) &quot;Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition.&quot; <i>J Cell Biol</i> <b>212</b>(3):349&ndash;64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26833789 26833789]; doi: [https://dx.doi.org/10.1083/jcb.201508080 10.1083/jcb.201508080]; GPMDB: [http://gpmdb.org/data/keyword/26833789 9].
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#Zhang P, Kirby D, Dufresne C, Chen Y, Turner R, Ferri S, Edward DP, Van Eyk JE, Semba RD,  (2016) &quot;Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid.&quot; <i>Proteomics</i> <b>16</b>(7):1146&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26834087 26834087]; doi: [https://dx.doi.org/10.1002/pmic.201500188 10.1002/pmic.201500188]; GPMDB: [http://gpmdb.org/data/keyword/26834087 120].
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#Long B, Muhamad R, Yan G, Yu J, Fan Q, Wang Z, Li X, Purnomoadi A, Achmadi J, Yan X,  (2016) &quot;Quantitative proteomics analysis reveals glutamine deprivation activates fatty acid &beta;-oxidation pathway in HepG2 cells.&quot; <i>Amino Acids</i> <b>48</b>(5):1297&ndash;307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26837383 26837383]; doi: [https://dx.doi.org/10.1007/s00726-016-2182-7 10.1007/s00726-016-2182-7]; GPMDB: [http://gpmdb.org/data/keyword/26837383 1].
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#Iwamoto N, D&#39;Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, B&ouml;hm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingm&uuml;ller U, Schilling M,  (2016) &quot;Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation.&quot; <i>Sci Signal</i> <b>9</b>(413):ra13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26838549 26838549]; doi: [https://dx.doi.org/10.1126/scisignal.aab1967 10.1126/scisignal.aab1967]; GPMDB: [http://gpmdb.org/data/keyword/26838549 66].
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#Tong M, Kleffmann T, Pradhan S, Johansson CL, DeSousa J, Stone PR, James JL, Chen Q, Chamley LW,  (2016) &quot;Proteomic characterization of macro-, micro- and nano-extracellular vesicles derived from the same first trimester placenta: relevance for feto-maternal communication.&quot; <i>Hum Reprod</i> <b>31</b>(4):687&ndash;99; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839151 26839151]; doi: [https://dx.doi.org/10.1093/humrep/dew004 10.1093/humrep/dew004]; GPMDB: [http://gpmdb.org/data/keyword/26839151 3].
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#Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA,  (2016) &quot;PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis.&quot; <i>Elife</i> <b>5</b>:e13292; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839287 26839287]; doi: [https://dx.doi.org/10.7554/eLife.13292 10.7554/eLife.13292]; GPMDB: [http://gpmdb.org/data/keyword/26839287 9].
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#Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD,  (2016) &quot;Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition.&quot; <i>Sci Rep</i> <b>6</b>:20455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26842662 26842662]; doi: [https://dx.doi.org/10.1038/srep20455 10.1038/srep20455]; GPMDB: [http://gpmdb.org/data/keyword/26842662 20].
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#Chidiac R, Zhang Y, Tessier S, Faubert D, Delisle C, Gratton JP,  (2016) &quot;Comparative Phosphoproteomics Analysis of VEGF and Angiopoietin-1 Signaling Reveals ZO-1 as a Critical Regulator of Endothelial Cell Proliferation.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1511&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26846344 26846344]; doi: [https://dx.doi.org/10.1074/mcp.M115.053298 10.1074/mcp.M115.053298]; GPMDB: [http://gpmdb.org/data/keyword/26846344 13].
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#Meierhofer D, Halbach M, &#x15E;en NE, Gispert S, Auburger G,  (2016) &quot;Ataxin-2 (Atxn2)-Knock-Out Mice Show Branched Chain Amino Acids and Fatty Acids Pathway Alterations.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1728&ndash;39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26850065 26850065]; doi: [https://dx.doi.org/10.1074/mcp.M115.056770 10.1074/mcp.M115.056770]; GPMDB: [http://gpmdb.org/data/keyword/26850065 48].
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#Aretz I, Hardt C, Wittig I, Meierhofer D,  (2016) &quot;An Impaired Respiratory Electron Chain Triggers Down-regulation of the Energy Metabolism and De-ubiquitination of Solute Carrier Amino Acid Transporters.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1526&ndash;38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26852163 26852163]; doi: [https://dx.doi.org/10.1074/mcp.M115.053181 10.1074/mcp.M115.053181]; GPMDB: [http://gpmdb.org/data/keyword/26852163 60].
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#Peffers MJ, Collins J, Fang Y, Goljanek-Whysall K, Rushton M, Loughlin J, Proctor C, Clegg PD,  (2016) &quot;Age-related changes in mesenchymal stem cells identified using a multi-omics approach.&quot; <i>Eur Cell Mater</i> <b>31</b>:136&ndash;59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26853623 26853623]; GPMDB: [http://gpmdb.org/data/keyword/26853623 8].
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#Billing AM, Ben Hamidane H, Dib SS, Cotton RJ, Bhagwat AM, Kumar P, Hayat S, Yousri NA, Goswami N, Suhre K, Rafii A, Graumann J,  (2016) &quot;Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers.&quot; <i>Sci Rep</i> <b>6</b>:21507; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26857143 26857143]; doi: [https://dx.doi.org/10.1038/srep21507 10.1038/srep21507]; GPMDB: [http://gpmdb.org/data/keyword/26857143 9].
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#Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Th&eacute;ry C,  (2016) &quot;Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes.&quot; <i>Proc Natl Acad Sci U S A</i> <b>113</b>(8):E968&ndash;77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26858453 26858453]; doi: [https://dx.doi.org/10.1073/pnas.1521230113 10.1073/pnas.1521230113]; GPMDB: [http://gpmdb.org/data/keyword/26858453 56].
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#Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, J&oslash;rgensen C,  (2016) &quot;Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration.&quot; <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76].
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#Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-D&uuml;rr P, Shah AM, Brandes RP,  (2016) &quot;The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein.&quot; <i>J Biol Chem</i> <b>291</b>(13):7045&ndash;59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80].
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#Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J,  (2016) &quot;Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency.&quot; <i>Proteomics</i> <b>16</b>(7):1166&ndash;76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50].
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#Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Ve&#x10D;erek B, Sebo P, Schmidt F, V&ouml;lker U, Rodriguez ME,  (2016) &quot;Proteome analysis of Bordetella pertussis isolated from human macrophages.&quot; <i>J Proteomics</i> <b>136</b>:55&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9].
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#Kn&ouml;ppel A, N&auml;svall J, Andersson DI,  (2016) &quot;Compensating the Fitness Costs of Synonymous Mutations.&quot; <i>Mol Biol Evol</i> <b>33</b>(6):1461&ndash;77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26882986 26882986]; doi: [https://dx.doi.org/10.1093/molbev/msw028 10.1093/molbev/msw028]; GPMDB: [http://gpmdb.org/data/keyword/26882986 72].
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#Creedon H, G&oacute;mez-Cuadrado L, Tarnauskait&#x117; &#x17D;, Balla J, Canel M, MacLeod KG, Serrels B, Fraser C, Unciti-Broceta A, Tracey N, Le Bihan T, Klinowska T, Sims AH, Byron A, Brunton VG,  (2016) &quot;Identification of novel pathways linking epithelial-to-mesenchymal transition with resistance to HER2-targeted therapy.&quot; <i>Oncotarget</i> <b>7</b>(10):11539&ndash;52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883193 26883193]; doi: [https://dx.doi.org/10.18632/oncotarget.7317 10.18632/oncotarget.7317]; GPMDB: [http://gpmdb.org/data/keyword/26883193 6].
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#Zufferey A, Ibberson M, Reny JL, Nolli S, Schvartz D, Docquier M, Xenarios I, Sanchez JC, Fontana P,  (2016) &quot;New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach.&quot; <i>Hum Genet</i> <b>135</b>(4):403&ndash;14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883867 26883867]; doi: [https://dx.doi.org/10.1007/s00439-016-1642-1 10.1007/s00439-016-1642-1]; GPMDB: [http://gpmdb.org/data/keyword/26883867 13].
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#Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T,  (2016) &quot;Deubiquitylation of Protein Cargo Is Not an Essential Step in Exosome Formation.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1556&ndash;71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26884507 26884507]; doi: [https://dx.doi.org/10.1074/mcp.M115.054965 10.1074/mcp.M115.054965]; GPMDB: [http://gpmdb.org/data/keyword/26884507 64].
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#Ramallo Guevara C, Philipp O, Hamann A, Werner A, Osiewacz HD, Rexroth S, R&ouml;gner M, Poetsch A,  (2016) &quot;Global Protein Oxidation Profiling Suggests Efficient Mitochondrial Proteome Homeostasis During Aging.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1692&ndash;709; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26884511 26884511]; doi: [https://dx.doi.org/10.1074/mcp.M115.055616 10.1074/mcp.M115.055616]; GPMDB: [http://gpmdb.org/data/keyword/26884511 17].
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#Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, Wang KY, Lin SY, Shih YL,  (2016) &quot;Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1572&ndash;83; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26889046 26889046]; doi: [https://dx.doi.org/10.1074/mcp.M115.053603 10.1074/mcp.M115.053603]; GPMDB: [http://gpmdb.org/data/keyword/26889046 4].
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#Hiramatsu K, Yoshino K, Serada S, Yoshihara K, Hori Y, Fujimoto M, Matsuzaki S, Egawa-Takata T, Kobayashi E, Ueda Y, Morii E, Enomoto T, Naka T, Kimura T,  (2016) &quot;Similar protein expression profiles of ovarian and endometrial high-grade serous carcinomas.&quot; <i>Br J Cancer</i> <b>114</b>(5):554&ndash;61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26889980 26889980]; doi: [https://dx.doi.org/10.1038/bjc.2016.27 10.1038/bjc.2016.27]; GPMDB: [http://gpmdb.org/data/keyword/26889980 6].
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#Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE,  (2016) &quot;Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1584&ndash;97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26896796 26896796]; doi: [https://dx.doi.org/10.1074/mcp.M115.054056 10.1074/mcp.M115.054056]; GPMDB: [http://gpmdb.org/data/keyword/26896796 4].
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#Zilkenat S, Franz-Wachtel M, Stierhof YD, Gal&aacute;n JE, Macek B, Wagner S,  (2016) &quot;Determination of the Stoichiometry of the Complete Bacterial Type III Secretion Needle Complex Using a Combined Quantitative Proteomic Approach.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1598&ndash;609; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26900162 26900162]; doi: [https://dx.doi.org/10.1074/mcp.M115.056598 10.1074/mcp.M115.056598]; GPMDB: [http://gpmdb.org/data/keyword/26900162 18].
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#Zhao L, Chen Y, Bajaj AO, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SY, He F, Li Y, Wensel TG, Qin J, Chen R,  (2016) &quot;Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes.&quot; <i>Genome Res</i> <b>26</b>(5):660&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912414 26912414]; doi: [https://dx.doi.org/10.1101/gr.198911.115 10.1101/gr.198911.115]; GPMDB: [http://gpmdb.org/data/keyword/26912414 26].
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#Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder E, Carr SA, Jaffe JD,  (2016) &quot;Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1622&ndash;41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912667 26912667]; doi: [https://dx.doi.org/10.1074/mcp.M116.058354 10.1074/mcp.M116.058354]; GPMDB: [http://gpmdb.org/data/keyword/26912667 4].
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#Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M,  (2016) &quot;In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1642&ndash;57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912668 26912668]; doi: [https://dx.doi.org/10.1074/mcp.M115.053975 10.1074/mcp.M115.053975]; GPMDB: [http://gpmdb.org/data/keyword/26912668 66].
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#Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M,  (2016) &quot;New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants.&quot; <i>J Proteomics</i> <b>138</b>:1&ndash;19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26915584 26915584]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.012 10.1016/j.jprot.2016.02.012]; GPMDB: [http://gpmdb.org/data/keyword/26915584 24].
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#Xu B, Gao Y, Zhan S, Xiong F, Qiu W, Qian X, Wang T, Wang N, Zhang D, Yang Q, Wang R, Bao X, Dou W, Tian R, Meng S, Gai WP, Huang Y, Yan XX, Ge W, Ma C,  (2016) &quot;Quantitative protein profiling of hippocampus during human aging.&quot; <i>Neurobiol Aging</i> <b>39</b>:46&ndash;56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26923401 26923401]; doi: [https://dx.doi.org/10.1016/j.neurobiolaging.2015.11.029 10.1016/j.neurobiolaging.2015.11.029]; GPMDB: [http://gpmdb.org/data/keyword/26923401 20].
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#de Torre-Minguela C, Barber&agrave;-Cremades M, G&oacute;mez AI, Mart&iacute;n-S&aacute;nchez F, Pelegr&iacute;n P,  (2016) &quot;Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process.&quot; <i>Sci Rep</i> <b>6</b>:22586; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26935289 26935289]; doi: [https://dx.doi.org/10.1038/srep22586 10.1038/srep22586]; GPMDB: [http://gpmdb.org/data/keyword/26935289 118].
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#Ly A, Merl-Pham J, Priller M, Gruhn F, Senninger N, Ueffing M, Hauck SM,  (2016) &quot;Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model.&quot; <i>J Proteome Res</i> <b>15</b>(4):1350&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26939627 26939627]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00111 10.1021/acs.jproteome.6b00111]; GPMDB: [http://gpmdb.org/data/keyword/26939627 24].
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#Salih M, Demmers JA, Bezstarosti K, Leonhard WN, Losekoot M, van Kooten C, Gansevoort RT, Peters DJ, Zietse R, Hoorn EJ, DIPAK Consortium,  (2016) &quot;Proteomics of Urinary Vesicles Links Plakins and Complement to Polycystic Kidney Disease.&quot; <i>J Am Soc Nephrol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26940098 26940098]; doi: [https://dx.doi.org/10.1681/ASN.2015090994 10.1681/ASN.2015090994]; GPMDB: [http://gpmdb.org/data/keyword/26940098 7].
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#Kamkina P, Snoek LB, Grossmann J, Volkers RJ, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE,  (2016) &quot;Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1670&ndash;80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26944343 26944343]; doi: [https://dx.doi.org/10.1074/mcp.M115.052548 10.1074/mcp.M115.052548]; GPMDB: [http://gpmdb.org/data/keyword/26944343 12].
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#Xin L, Xu B, Ma L, Hou Q, Ye M, Meng S, Ding X, Ge W,  (2016) &quot;Proteomics study reveals that the dysregulation of focal adhesion and ribosome contribute to early pregnancy loss.&quot; <i>Proteomics Clin Appl</i> <b>10</b>(5):554&ndash;63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26947931 26947931]; doi: [https://dx.doi.org/10.1002/prca.201500136 10.1002/prca.201500136]; GPMDB: [http://gpmdb.org/data/keyword/26947931 1].
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#Adewole OO, Erhabor GE, Adewole TO, Ojo AO, Oshokoya H, Wolfe LM, Prenni JE,  (2016) &quot;Proteomic profiling of eccrine sweat reveals its potential as a diagnostic biofluid for active tuberculosis.&quot; <i>Proteomics Clin Appl</i> <b>10</b>(5):547&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26948146 26948146]; doi: [https://dx.doi.org/10.1002/prca.201500071 10.1002/prca.201500071]; GPMDB: [http://gpmdb.org/data/keyword/26948146 10].
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#Lai ZW, Bolm L, Fuellgraf H, Biniossek ML, Makowiec F, Hopt UT, Werner M, Keck T, Bausch D, Sorio C, Scarpa A, Schilling O, Bronsert P, Wellner UF,  (2016) &quot;Characterization of various cell lines from different ampullary cancer subtypes and cancer associated fibroblast-mediated responses.&quot; <i>BMC Cancer</i> <b>16</b>:195; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26951071 26951071]; doi: [https://dx.doi.org/10.1186/s12885-016-2193-5 10.1186/s12885-016-2193-5]; GPMDB: [http://gpmdb.org/data/keyword/26951071 5].
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#De Marchi T, Kuhn E, Dekker LJ, Stingl C, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Luider TM, Foekens JA, Martens JW, Carr SA, Umar A,  (2016) &quot;Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera.&quot; <i>J Proteome Res</i> <b>15</b>(4):1230&ndash;42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26958999 26958999]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01119 10.1021/acs.jproteome.5b01119]; GPMDB: [http://gpmdb.org/data/keyword/26958999 78].
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#Jo DH, Bae J, Chae S, Kim JH, Han JH, Hwang D, Lee SW, Kim JH,  (2016) &quot;Quantitative Proteomics Reveals &beta;2 Integrin-mediated Cytoskeletal Rearrangement in Vascular Endothelial Growth Factor (VEGF)-induced Retinal Vascular Hyperpermeability.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(5):1681&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26969716 26969716]; doi: [https://dx.doi.org/10.1074/mcp.M115.053249 10.1074/mcp.M115.053249]; GPMDB: [http://gpmdb.org/data/keyword/26969716 72].
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#Gallart-Palau X, Lee BS, Adav SS, Qian J, Serra A, Park JE, Lai MK, Chen CP, Kalaria RN, Sze SK,  (2016) &quot;Gender differences in white matter pathology and mitochondrial dysfunction in Alzheimer&#39;s disease with cerebrovascular disease.&quot; <i>Mol Brain</i> <b>9</b>:27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26983404 26983404]; doi: [https://dx.doi.org/10.1186/s13041-016-0205-7 10.1186/s13041-016-0205-7]; GPMDB: [http://gpmdb.org/data/keyword/26983404 10].
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#Bonn F, Pan&eacute;-Farr&eacute; J, Schl&uuml;ter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, V&ouml;lker U, van Dijl JM, Hecker M, M&auml;der U, Becher D,  (2016) &quot;Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300.&quot; <i>Int J Med Microbiol</i> <b>306</b>(3):131&ndash;40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26996810 26996810]; doi: [https://dx.doi.org/10.1016/j.ijmm.2016.02.004 10.1016/j.ijmm.2016.02.004]; GPMDB: [http://gpmdb.org/data/keyword/26996810 300].
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#He JJ, Ma J, Elsheikha HM, Song HQ, Zhou DH, Zhu XQ,  (2016) &quot;Proteomic Profiling of Mouse Liver following Acute Toxoplasma gondii Infection.&quot; <i>PLoS One</i> <b>11</b>(3):e0152022; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27003162 27003162]; doi: [https://dx.doi.org/10.1371/journal.pone.0152022 10.1371/journal.pone.0152022]; GPMDB: [http://gpmdb.org/data/keyword/27003162 1].
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#Li&ntilde;eiro E, Chiva C, Cantoral JM, Sabido E, Fern&aacute;ndez-Acero FJ,  (2016) &quot;Phosphoproteome analysis of B. cinerea in response to different plant-based elicitors.&quot; <i>J Proteomics</i> <b>139</b>:84&ndash;94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27003611 27003611]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.019 10.1016/j.jprot.2016.03.019]; GPMDB: [http://gpmdb.org/data/keyword/27003611 8].
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#Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher DF, Coon JJ,  (2016) &quot;The Peripheral Blood Eosinophil Proteome.&quot; <i>J Proteome Res</i> <b>15</b>(5):1524&ndash;33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27005946 27005946]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00006 10.1021/acs.jproteome.6b00006]; GPMDB: [http://gpmdb.org/data/keyword/27005946 45].
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#Wilson MC, Trakarnsanga K, Heesom KJ, Cogan N, Green C, Toye AM, Parsons SF, Anstee DJ, Frayne J,  (2016) &quot;Comparison of the Proteome of Adult and Cord Erythroid Cells, and Changes in the Proteome Following Reticulocyte Maturation.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(6):1938&ndash;46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27006477 27006477]; doi: [https://dx.doi.org/10.1074/mcp.M115.057315 10.1074/mcp.M115.057315]; GPMDB: [http://gpmdb.org/data/keyword/27006477 2].
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#Sunitha B, Gayathri N, Kumar M, Keshava Prasad TS, Nalini A, Padmanabhan B, Srinivas Bharath MM,  (2016) &quot;Muscle biopsies from human muscle diseases with myopathic pathology reveal common alterations in mitochondrial function.&quot; <i>J Neurochem</i> <b>138</b>(1):174&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27015874 27015874]; doi: [https://dx.doi.org/10.1111/jnc.13626 10.1111/jnc.13626]; GPMDB: [http://gpmdb.org/data/keyword/27015874 1].
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#Huang D, Piening BD, Kennedy JJ, Lin C, Jones-Weinert CW, Yan P, Paulovich AG,  (2016) &quot;DNA Replication Stress Phosphoproteome Profiles Reveal Novel Functional Phosphorylation Sites on Xrs2 in Saccharomyces cerevisiae.&quot; <i>Genetics</i> <b>203</b>(1):353&ndash;68; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27017623 27017623]; doi: [https://dx.doi.org/10.1534/genetics.115.185231 10.1534/genetics.115.185231]; GPMDB: [http://gpmdb.org/data/keyword/27017623 4].
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#Slany A, Bileck A, Kreutz D, Mayer RL, Muqaku B, Gerner C,  (2016) &quot;Contribution of Human Fibroblasts and Endothelial Cells to the Hallmarks of Inflammation as Determined by Proteome Profiling.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(6):1982&ndash;97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025457 27025457]; doi: [https://dx.doi.org/10.1074/mcp.M116.058099 10.1074/mcp.M116.058099]; GPMDB: [http://gpmdb.org/data/keyword/27025457 104].
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#Osinalde N, S&aacute;nchez-Quiles V, Blagoev B, Kratchmarova I,  (2016) &quot;Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes.&quot; <i>Sci Rep</i> <b>6</b>:23530; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025927 27025927]; doi: [https://dx.doi.org/10.1038/srep23530 10.1038/srep23530]; GPMDB: [http://gpmdb.org/data/keyword/27025927 22].
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#Xu G, Pattamatta A, Hildago R, Pace MC, Brown H, Borchelt DR,  (2016) &quot;Vulnerability of newly synthesized proteins to proteostasis stress.&quot; <i>J Cell Sci</i> <b>129</b>(9):1892&ndash;901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27026526 27026526]; doi: [https://dx.doi.org/10.1242/jcs.176479 10.1242/jcs.176479]; GPMDB: [http://gpmdb.org/data/keyword/27026526 55].
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#Salvetti A, Cout&eacute; Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A,  (2016) &quot;Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches.&quot; <i>J Proteome Res</i> <b>15</b>(5):1659&ndash;69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27049334 27049334]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00126 10.1021/acs.jproteome.6b00126]; GPMDB: [http://gpmdb.org/data/keyword/27049334 7].
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#Zhou S, Okekeogbu I, Sangireddy S, Ye Z, Li H, Bhatti S, Hui D, McDonald DW, Yang Y, Giri S, Howe KJ, Fish T, Thannhauser TW,  (2016) &quot;Proteome Modification in Tomato Plants upon Long-Term Aluminum Treatment.&quot; <i>J Proteome Res</i> <b>15</b>(5):1670&ndash;84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27052409 27052409]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00128 10.1021/acs.jproteome.6b00128]; GPMDB: [http://gpmdb.org/data/keyword/27052409 68].
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#Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB,  (2016) &quot;Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(6):2021&ndash;32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27056914 27056914]; doi: [https://dx.doi.org/10.1074/mcp.M115.057240 10.1074/mcp.M115.057240]; GPMDB: [http://gpmdb.org/data/keyword/27056914 2].
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#Drabovich AP, Pavlou MP, Schiza C, Diamandis EP,  (2016) &quot;Dynamics of Protein Expression Reveals Primary Targets and Secondary Messengers of Estrogen Receptor Alpha Signaling in MCF-7 Breast Cancer Cells.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(6):2093&ndash;107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067054 27067054]; doi: [https://dx.doi.org/10.1074/mcp.M115.057257 10.1074/mcp.M115.057257]; GPMDB: [http://gpmdb.org/data/keyword/27067054 12].
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#Xu B, Tian R, Wang X, Zhan S, Wang R, Guo Y, Ge W,  (2016) &quot;Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury.&quot; <i>Brain Res</i> <b>1642</b>:344&ndash;52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067185 27067185]; doi: [https://dx.doi.org/10.1016/j.brainres.2016.04.008 10.1016/j.brainres.2016.04.008]; GPMDB: [http://gpmdb.org/data/keyword/27067185 20].
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#Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL,  (2016) &quot;Regulation of Platelet Derived Growth Factor Signaling by Leukocyte Common Antigen-related (LAR) Protein Tyrosine Phosphatase: A Quantitative Phosphoproteomics Study.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(6):1823&ndash;36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27074791 27074791]; doi: [https://dx.doi.org/10.1074/mcp.M115.053652 10.1074/mcp.M115.053652]; GPMDB: [http://gpmdb.org/data/keyword/27074791 17].
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#Lochmatter C, Fischer R, Charles PD, Yu Z, Powrie F, Kessler BM,  (2016) &quot;Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes.&quot; <i>Sci Rep</i> <b>6</b>:24491; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27080861 27080861]; doi: [https://dx.doi.org/10.1038/srep24491 10.1038/srep24491]; GPMDB: [http://gpmdb.org/data/keyword/27080861 7].
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#Arts IS, Vertommen D, Baldin F, Laloux G, Collet JF,  (2016) &quot;Comprehensively Characterizing the Thioredoxin Interactome In Vivo Highlights the Central Role Played by This Ubiquitous Oxidoreductase in Redox Control.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(6):2125&ndash;40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27081212 27081212]; doi: [https://dx.doi.org/10.1074/mcp.M115.056440 10.1074/mcp.M115.056440]; GPMDB: [http://gpmdb.org/data/keyword/27081212 103].
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#Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E,  (2016) &quot;Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes.&quot; <i>Cardiovasc Res</i> <b>110</b>(3):346&ndash;58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12].
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#Aaseb&oslash; E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud &Oslash;, Hernandez-Valladares M,  (2016) &quot;Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows.&quot; <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163].
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#Larance M, Kirkwood KJ, Tinti M, Murillo AB, Ferguson MA, Lamond AI,  (2016) &quot;Global Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27114452 27114452]; doi: [https://dx.doi.org/10.1074/mcp.O115.055467 10.1074/mcp.O115.055467]; GPMDB: [http://gpmdb.org/data/keyword/27114452 396].
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#Petrone A, Adamo ME, Cheg C, Kettenbach AN,  (2016) &quot;Identification of candidate CDK1 substrates in mitosis by quantitative phosphoproteomics.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27134283 27134283]; doi: [https://dx.doi.org/10.1074/mcp.M116.059394 10.1074/mcp.M116.059394]; GPMDB: [http://gpmdb.org/data/keyword/27134283 90].
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#Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M,  (2015) &quot;Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.&quot; <i>Cell Syst</i> <b>1</b>(3):224&ndash;37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190].
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#Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC,  (2016) &quot;Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice.&quot; <i>EMBO Mol Med</i> <b>8</b>(6):643&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120].
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#Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE,  (2016) &quot;Proteomics-driven antigen discovery for development of vaccines against gonorrhea.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3].
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#Masuishi Y, Kimura Y, Arakawa N, Hirano H,  (2016) &quot;Data for identification of GPI-anchored peptides and &omega;-sites in cancer cell lines.&quot; <i>Data Brief</i> <b>7</b>:1302&ndash;5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141528 27141528]; doi: [https://dx.doi.org/10.1016/j.dib.2016.04.001 10.1016/j.dib.2016.04.001]; GPMDB: [http://gpmdb.org/data/keyword/27141528 42].
 +
#Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA Jr, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM,  (2016) &quot;The pathogenesis of demyelinating form of Guillain-Barre syndrome: proteo-peptidomic and immunological profiling of physiological fluids.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27143409 27143409]; doi: [https://dx.doi.org/10.1074/mcp.M115.056036 10.1074/mcp.M115.056036]; GPMDB: [http://gpmdb.org/data/keyword/27143409 28].
 +
#Kempf SJ, Metaxas A, Ib&aacute;&ntilde;ez-Vea M, Darvesh S, Finsen B, Larsen MR,  (2016) &quot;An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer&#39;s mouse model.&quot; <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104].
 +
#D&oslash;rum S, Steinsb&oslash; &Oslash;, Bergseng E, Arntzen M&Oslash;, de Souza GA, Sollid LM,  (2016) &quot;Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes.&quot; <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27].
 +
#Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, KrishnaKumaar L, Samal A, Rao KV, Kumar D, Nandicoori VK,  (2016) &quot;Comparative proteomic analyses of avirulent, virulent and clinical strains of Mycobacterium tuberculosis identifies strain-specific patterns.&quot; <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16].
 +
#Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ,  (2016) &quot;Identification and characterization of potential biomarkers by quantitative tissue proteomics of primary lung adenocarcinoma.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27161446 27161446]; doi: [https://dx.doi.org/10.1074/mcp.M115.057026 10.1074/mcp.M115.057026]; GPMDB: [http://gpmdb.org/data/keyword/27161446 60].
 +
#Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Ch&acirc;telet I, Prior K, Harmsen D, Vogel U,  (2016) &quot;Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men.&quot; <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12].
 +
#Tuveng TR, Arntzen M&Oslash;, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG,  (2016) &quot;Proteomic investigation of the secretome of cellvibrio japonicus during growth on chitin.&quot; <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18].
 +
#Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M,  (2016) &quot;The clathrin-dependent spindle proteome.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130].
 +
#Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA,  (2016) &quot;Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex.&quot; <i>Cell Rep</i> <b>15</b>(8):1782&ndash;94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4].
 +
#Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA,  (2016) &quot;Human aqueous humor proteome in cataract, glaucoma and pseudoexfoliation syndrome.&quot; <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86].
 +
#Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson L, Barnes S, Goldman JE, Muddiman DC, Brenner M,  (2016) &quot;Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease.&quot; <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8].
 +
#Yang W, Jackson B, Zhang H,  (2016) &quot;Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics.&quot; <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12].
 +
#Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM,  (2016) &quot;Distinctive proteomic profiles among different regions of human carotid plaques in men and women.&quot; <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60].
 +
#Virant-Klun I, Leicht S, Hughes C, Krijgsveld J,  (2016) &quot;Identification of maturation-specific proteins by single-cell proteomics of human oocytes.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18].
 +
#Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S,  (2016) &quot;Biomarker Panel for Chronic Graft-Versus-Host Disease.&quot; <i>J Clin Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3].
 +
#Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M,  (2016) &quot;Proteomic analysis of mouse oocytes identifies PRMT7 as reprogramming factor that replaces SOX2 in the induction of pluripotent stem cells.&quot; <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14].
 +
#Lodrini M, Poschmann G, Schmidt V, W&uuml;nschel J, Dreidax D, Witt O, H&ouml;fer T, Meyer HE, St&uuml;hler K, Eggert A, Deubzer HE,  (2016) &quot;Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells.&quot; <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12].
 +
#Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL,  (2016) &quot;Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1.&quot; <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14].
 +
#Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S,  (2016) &quot;In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability.&quot; <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [http://gpmdb.org/data/keyword/27246970 25].
 +
#Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Feny&ouml; D, Ellis MJ, Carr SA, NCI CPTAC,  (2016) &quot;Proteogenomics connects somatic mutations to signalling in breast cancer.&quot; <i>Nature</i> <b>534</b>(7605):55&ndash;62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265].
 +
#Humphrey ES, Su SP, Nagrial AM, Hochgr&auml;fe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ,  (2016) &quot;Resolution of novel pancreatic ductal adenocarcinoma subtypes by global phosphotyrosine profiling.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112].
 +
#Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W,  (2016) &quot;Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer.&quot; <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2].
 +
#Prendergast L, M&uuml;ller S, Liu Y, Huang H, Dingli F, Loew D, Vassias I, Patel DJ, Sullivan KF, Almouzni G,  (2016) &quot;The CENP-T/-W complex is a binding partner of the histone chaperone FACT.&quot; <i>Genes Dev</i> <b>30</b>(11):1313&ndash;26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27284163 27284163]; doi: [https://dx.doi.org/10.1101/gad.275073.115 10.1101/gad.275073.115]; GPMDB: [http://gpmdb.org/data/keyword/27284163 47].

Revision as of 02:40, 27 June 2016

GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.

Contents

Current Public Data Sources

The following public data repositories are checked daily for new suitable raw data for reanalysis:

  1. ProteomeXchange/PRIDE;
  2. MASSIVE;
  3. PeptideAtlas/PASSEL;
  4. ProteomicsDB;
  5. The Chorus Project; and
  6. iProX.

Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.

Previous Data Sources

GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.

Review process

Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.

Data from publications

The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of June 26, 2016.

  1. Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." Infect Immun 57(3):999–1001; PMID: 2645217; GPMDB: 66.
  2. Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." Proc Natl Acad Sci U S A 99(17):11049–54; PMID: 12177431; doi: 10.1073/pnas.172170199; GPMDB: 498.
  3. Liu T, Qian WJ, Strittmatter EF, Camp DG 2nd, Anderson GA, Thrall BD, Smith RD, (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Anal Chem 76(18):5345–53; PMID: 15362891; doi: 10.1021/ac049485q; GPMDB: 6.
  4. Sauer G, Körner R, Hanisch A, Ries A, Nigg EA, Silljé HH, (2005) "Proteome analysis of the human mitotic spindle." Mol Cell Proteomics 4(1):35–43; PMID: 15561729; doi: 10.1074/mcp.M400158-MCP200; GPMDB: 1.
  5. Klein C, Garcia-Rizo C, Bisle B, Scheffer B, Zischka H, Pfeiffer F, Siedler F, Oesterhelt D, (2005) "The membrane proteome of Halobacterium salinarum." Proteomics 5(1):180–97; PMID: 15619294; doi: 10.1002/pmic.200400943; GPMDB: 37.
  6. Searle BC, Dasari S, Wilmarth PA, Turner M, Reddy AP, David LL, Nagalla SR, (2005) "Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm." J Proteome Res 4(2):546–54; PMID: 15822933; doi: 10.1021/pr049781j; GPMDB: 4.
  7. Elias JE, Haas W, Faherty BK, Gygi SP, (2005) "Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations." Nat Methods 2(9):667–75; PMID: 16118637; doi: 10.1038/nmeth785; GPMDB: 30.
  8. Lee YJ, Rice RH, Lee YM, (2006) "Proteome analysis of human hair shaft: from protein identification to posttranslational modification." Mol Cell Proteomics 5(5):789–800; PMID: 16446289; doi: 10.1074/mcp.M500278-MCP200; GPMDB: 75.
  9. Gatlin CL, Pieper R, Huang ST, Mongodin E, Gebregeorgis E, Parmar PP, Clark DJ, Alami H, Papazisi L, Fleischmann RD, Gill SR, Peterson SN, (2006) "Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus." Proteomics 6(5):1530–49; PMID: 16470658; doi: 10.1002/pmic.200500253; GPMDB: 1603.
  10. Keshamouni VG, Michailidis G, Grasso CS, Anthwal S, Strahler JR, Walker A, Arenberg DA, Reddy RC, Akulapalli S, Thannickal VJ, Standiford TJ, Andrews PC, Omenn GS, (2006) "Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype." J Proteome Res 5(5):1143–54; PMID: 16674103; doi: 10.1021/pr050455t; GPMDB: 3.
  11. Bisle B, Schmidt A, Scheibe B, Klein C, Tebbe A, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D, (2006) "Quantitative profiling of the membrane proteome in a halophilic archaeon." Mol Cell Proteomics 5(9):1543–58; PMID: 16804162; doi: 10.1074/mcp.M600106-MCP200; GPMDB: 32.
  12. Hamacher M, Apweiler R, Arnold G, Becker A, Blüggel M, Carrette O, Colvis C, Dunn MJ, Fröhlich T, Fountoulakis M, van Hall A, Herberg F, Ji J, Kretzschmar H, Lewczuk P, Lubec G, Marcus K, Martens L, Palacios Bustamante N, Park YM, Pennington SR, Robben J, Stühler K, Reidegeld KA, Riederer P, Rossier J, Sanchez JC, Schrader M, Stephan C, Tagle D, Thiele H, Wang J, Wiltfang J, Yoo JS, Zhang C, Klose J, Meyer HE, (2006) "HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy." Proteomics 6(18):4890–8; PMID: 16927433; doi: 10.1002/pmic.200600295; GPMDB: 296.
  13. Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP, (2006) "A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Nat Biotechnol 24(10):1285–92; PMID: 16964243; doi: 10.1038/nbt1240; GPMDB: 31.
  14. Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS, (2006) "An integrated systems approach for understanding cellular responses to gamma radiation." Mol Syst Biol 2:47; PMID: 16969339; doi: 10.1038/msb4100091; GPMDB: 27.
  15. Price TS, Lucitt MB, Wu W, Austin DJ, Pizarro A, Yocum AK, Blair IA, FitzGerald GA, Grosser T, (2007) "EBP, a program for protein identification using multiple tandem mass spectrometry datasets." Mol Cell Proteomics 6(3):527–36; PMID: 17164401; doi: 10.1074/mcp.T600049-MCP200; GPMDB: 314.
  16. Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V, (2007) "Improving gene annotation using peptide mass spectrometry." Genome Res 17(2):231–9; PMID: 17189379; doi: 10.1101/gr.5646507; GPMDB: 1.
  17. Konstantinidis K, Tebbe A, Klein C, Scheffer B, Aivaliotis M, Bisle B, Falb M, Pfeiffer F, Siedler F, Oesterhelt D, (2007) "Genome-wide proteomics of Natronomonas pharaonis." J Proteome Res 6(1):185–93; PMID: 17203963; doi: 10.1021/pr060352q; GPMDB: 176.
  18. Villén J, Beausoleil SA, Gerber SA, Gygi SP, (2007) "Large-scale phosphorylation analysis of mouse liver." Proc Natl Acad Sci U S A 104(5):1488–93; PMID: 17242355; doi: 10.1073/pnas.0609836104; GPMDB: 1.
  19. Klein C, Aivaliotis M, Olsen JV, Falb M, Besir H, Scheffer B, Bisle B, Tebbe A, Konstantinidis K, Siedler F, Pfeiffer F, Mann M, Oesterhelt D, (2007) "The low molecular weight proteome of Halobacterium salinarum." J Proteome Res 6(4):1510–8; PMID: 17326674; doi: 10.1021/pr060634q; GPMDB: 10.
  20. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC, (2007) "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry." Science 316(5822):280–5; PMID: 17431180; doi: 10.1126/science.1137614; GPMDB: 2.
  21. Lowery DM, Clauser KR, Hjerrild M, Lim D, Alexander J, Kishi K, Ong SE, Gammeltoft S, Carr SA, Yaffe MB, (2007) "Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate." EMBO J 26(9):2262–73; PMID: 17446864; doi: 10.1038/sj.emboj.7601683; GPMDB: 24.
  22. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R, (2007) "A high-quality catalog of the Drosophila melanogaster proteome." Nat Biotechnol 25(5):576–83; PMID: 17450130; doi: 10.1038/nbt1300; GPMDB: 1907.
  23. Wu L, Hwang SI, Rezaul K, Lu LJ, Mayya V, Gerstein M, Eng JK, Lundgren DH, Han DK, (2007) "Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling." Mol Cell Proteomics 6(8):1343–53; PMID: 17519225; doi: 10.1074/mcp.M700017-MCP200; GPMDB: 2299.
  24. Au CE, Bell AW, Gilchrist A, Hiding J, Nilsson T, Bergeron JJ, (2007) "Organellar proteomics to create the cell map." Curr Opin Cell Biol 19(4):376–85; PMID: 17689063; doi: 10.1016/j.ceb.2007.05.004; GPMDB: 4090.
  25. Whiteaker JR, Zhang H, Zhao L, Wang P, Kelly-Spratt KS, Ivey RG, Piening BD, Feng LC, Kasarda E, Gurley KE, Eng JK, Chodosh LA, Kemp CJ, McIntosh MW, Paulovich AG, (2007) "Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer." J Proteome Res 6(10):3962–75; PMID: 17711321; doi: 10.1021/pr070202v; GPMDB: 84.
  26. Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, Hobson S, Mathieson T, Perrin J, Raida M, Rau C, Reader V, Sweetman G, Bauer A, Bouwmeester T, Hopf C, Kruse U, Neubauer G, Ramsden N, Rick J, Kuster B, Drewes G, (2007) "Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors." Nat Biotechnol 25(9):1035–44; PMID: 17721511; doi: 10.1038/nbt1328; GPMDB: 729.
  27. Padliya ND, Garrett WM, Campbell KB, Tabb DL, Cooper B, (2007) "Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences." Proteomics 7(21):3932–42; PMID: 17922518; doi: 10.1002/pmic.200700419; GPMDB: 1.
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