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==Data from publications== | ==Data from publications== | ||
- | The following is a list of 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 December | + | The following is a list of 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 December 25, 2016. |
#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." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #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." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Krisp C, Yang H, van Soest R, Molloy MP, (2015) "Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(6):1708–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850434 25850434]; doi: [https://dx.doi.org/10.1074/mcp.M114.046425 10.1074/mcp.M114.046425]; GPMDB: [http://gpmdb.org/data/keyword/25850434 12]. | #Krisp C, Yang H, van Soest R, Molloy MP, (2015) "Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(6):1708–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850434 25850434]; doi: [https://dx.doi.org/10.1074/mcp.M114.046425 10.1074/mcp.M114.046425]; GPMDB: [http://gpmdb.org/data/keyword/25850434 12]. | ||
#Stuart SA, Houel S, Lee T, Wang N, Old WM, Ahn NG, (2015) "A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells." <i>Mol Cell Proteomics</i> <b>14</b>(6):1599–615; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850435 25850435]; doi: [https://dx.doi.org/10.1074/mcp.M114.047233 10.1074/mcp.M114.047233]; GPMDB: [http://gpmdb.org/data/keyword/25850435 255]. | #Stuart SA, Houel S, Lee T, Wang N, Old WM, Ahn NG, (2015) "A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells." <i>Mol Cell Proteomics</i> <b>14</b>(6):1599–615; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850435 25850435]; doi: [https://dx.doi.org/10.1074/mcp.M114.047233 10.1074/mcp.M114.047233]; GPMDB: [http://gpmdb.org/data/keyword/25850435 255]. | ||
+ | #Bergner SV, Scholz M, Trompelt K, Barth J, Gäbelein P, Steinbeck J, Xue H, Clowez S, Fucile G, Goldschmidt-Clermont M, Fufezan C, Hippler M, (2015) "STATE TRANSITION7-Dependent Phosphorylation Is Modulated by Changing Environmental Conditions, and Its Absence Triggers Remodeling of Photosynthetic Protein Complexes." <i>Plant Physiol</i> <b>168</b>(2):615–34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25858915 25858915]; doi: [https://dx.doi.org/10.1104/pp.15.00072 10.1104/pp.15.00072]; GPMDB: [http://gpmdb.org/data/keyword/25858915 72]. | ||
#Oberstein A, Perlman DH, Shenk T, Terry LJ, (2015) "Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome." <i>Proteomics</i> <b>15</b>(12):2006–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25867546 25867546]; doi: [https://dx.doi.org/10.1002/pmic.201400607 10.1002/pmic.201400607]; GPMDB: [http://gpmdb.org/data/keyword/25867546 8]. | #Oberstein A, Perlman DH, Shenk T, Terry LJ, (2015) "Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome." <i>Proteomics</i> <b>15</b>(12):2006–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25867546 25867546]; doi: [https://dx.doi.org/10.1002/pmic.201400607 10.1002/pmic.201400607]; GPMDB: [http://gpmdb.org/data/keyword/25867546 8]. | ||
#Papadopoulos P, Gutiérrez L, Demmers J, Scheer E, Pourfarzad F, Papageorgiou DN, Karkoulia E, Strouboulis J, van de Werken HJ, van der Linden R, Vandenberghe P, Dekkers DH, Philipsen S, Grosveld F, Tora L, (2015) "TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis." <i>Mol Cell Biol</i> <b>35</b>(12):2103–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25870109 25870109]; doi: [https://dx.doi.org/10.1128/MCB.01370-14 10.1128/MCB.01370-14]; GPMDB: [http://gpmdb.org/data/keyword/25870109 4]. | #Papadopoulos P, Gutiérrez L, Demmers J, Scheer E, Pourfarzad F, Papageorgiou DN, Karkoulia E, Strouboulis J, van de Werken HJ, van der Linden R, Vandenberghe P, Dekkers DH, Philipsen S, Grosveld F, Tora L, (2015) "TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis." <i>Mol Cell Biol</i> <b>35</b>(12):2103–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25870109 25870109]; doi: [https://dx.doi.org/10.1128/MCB.01370-14 10.1128/MCB.01370-14]; GPMDB: [http://gpmdb.org/data/keyword/25870109 4]. | ||
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#Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D, (2015) "Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions." <i>J Proteome Res</i> <b>14</b>(9):3804–22; 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]. | #Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D, (2015) "Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions." <i>J Proteome Res</i> <b>14</b>(9):3804–22; 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]. | ||
#Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar 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) "An open-source computational and data resource to analyze digital maps of immunopeptidomes." <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]. | #Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar 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) "An open-source computational and data resource to analyze digital maps of immunopeptidomes." <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]. | ||
+ | #Madsen CT, Sylvestersen KB, Young C, Larsen SC, Poulsen JW, Andersen MA, Palmqvist EA, Hey-Mogensen M, Jensen PB, Treebak JT, Lisby M, Nielsen ML, (2015) "Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p." <i>Nat Commun</i> <b>6</b>:7726; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26158509 26158509]; doi: [https://dx.doi.org/10.1038/ncomms8726 10.1038/ncomms8726]; GPMDB: [http://gpmdb.org/data/keyword/26158509 47]. | ||
#Stroud DA, Maher MJ, Lindau C, Vögtle FN, Frazier AE, Surgenor E, Mountford H, Singh AP, Bonas M, Oeljeklaus S, Warscheid B, Meisinger C, Thorburn DR, Ryan MT, (2015) "COA6 is a mitochondrial complex IV assembly factor critical for biogenesis of mtDNA-encoded COX2." <i>Hum Mol Genet</i> <b>24</b>(19):5404–15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26160915 26160915]; doi: [https://dx.doi.org/10.1093/hmg/ddv265 10.1093/hmg/ddv265]; GPMDB: [http://gpmdb.org/data/keyword/26160915 14]. | #Stroud DA, Maher MJ, Lindau C, Vögtle FN, Frazier AE, Surgenor E, Mountford H, Singh AP, Bonas M, Oeljeklaus S, Warscheid B, Meisinger C, Thorburn DR, Ryan MT, (2015) "COA6 is a mitochondrial complex IV assembly factor critical for biogenesis of mtDNA-encoded COX2." <i>Hum Mol Genet</i> <b>24</b>(19):5404–15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26160915 26160915]; doi: [https://dx.doi.org/10.1093/hmg/ddv265 10.1093/hmg/ddv265]; GPMDB: [http://gpmdb.org/data/keyword/26160915 14]. | ||
#Jumeau F, Com E, Lane L, Duek P, Lagarrigue M, Lavigne R, Guillot L, Rondel K, Gateau A, Melaine N, Guével B, Sergeant N, Mitchell V, Pineau C, (2015) "Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3606–20; 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]. | #Jumeau F, Com E, Lane L, Duek P, Lagarrigue M, Lavigne R, Guillot L, Rondel K, Gateau A, Melaine N, Guével B, Sergeant N, Mitchell V, Pineau C, (2015) "Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3606–20; 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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#McAfee A, Harpur BA, Michaud S, Beavis RC, Kent CF, Zayed A, Foster LJ, (2016) "Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics." <i>J Proteome Res</i> <b>15</b>(2):411–21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26718741 26718741]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00589 10.1021/acs.jproteome.5b00589]; GPMDB: [http://gpmdb.org/data/keyword/26718741 27]. | #McAfee A, Harpur BA, Michaud S, Beavis RC, Kent CF, Zayed A, Foster LJ, (2016) "Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics." <i>J Proteome Res</i> <b>15</b>(2):411–21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26718741 26718741]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00589 10.1021/acs.jproteome.5b00589]; GPMDB: [http://gpmdb.org/data/keyword/26718741 27]. | ||
#Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV, (2016) "Protein turnover during in vitro tissue engineering." <i>Biomaterials</i> <b>81</b>:104–13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26724458 26724458]; doi: [https://dx.doi.org/10.1016/j.biomaterials.2015.12.004 10.1016/j.biomaterials.2015.12.004]; GPMDB: [http://gpmdb.org/data/keyword/26724458 66]. | #Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV, (2016) "Protein turnover during in vitro tissue engineering." <i>Biomaterials</i> <b>81</b>:104–13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26724458 26724458]; doi: [https://dx.doi.org/10.1016/j.biomaterials.2015.12.004 10.1016/j.biomaterials.2015.12.004]; GPMDB: [http://gpmdb.org/data/keyword/26724458 66]. | ||
- | #Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, (2016) "Proteomic maps of breast cancer subtypes." <i>Nat Commun</i> <b>7</b>:10259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26725330 26725330]; doi: [https://dx.doi.org/10.1038/ncomms10259 10.1038/ncomms10259]; GPMDB: [http://gpmdb.org/data/keyword/26725330 | + | #Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, (2016) "Proteomic maps of breast cancer subtypes." <i>Nat Commun</i> <b>7</b>:10259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26725330 26725330]; doi: [https://dx.doi.org/10.1038/ncomms10259 10.1038/ncomms10259]; GPMDB: [http://gpmdb.org/data/keyword/26725330 255]. |
#Laumont CM, Daouda T, Laverdure JP, Bonneil É, Caron-Lizotte O, Hardy MP, Granados DP, Durette C, Lemieux S, Thibault P, Perreault C, (2016) "Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames." <i>Nat Commun</i> <b>7</b>:10238; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728094 26728094]; doi: [https://dx.doi.org/10.1038/ncomms10238 10.1038/ncomms10238]; GPMDB: [http://gpmdb.org/data/keyword/26728094 35]. | #Laumont CM, Daouda T, Laverdure JP, Bonneil É, Caron-Lizotte O, Hardy MP, Granados DP, Durette C, Lemieux S, Thibault P, Perreault C, (2016) "Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames." <i>Nat Commun</i> <b>7</b>:10238; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728094 26728094]; doi: [https://dx.doi.org/10.1038/ncomms10238 10.1038/ncomms10238]; GPMDB: [http://gpmdb.org/data/keyword/26728094 35]. | ||
#Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, (2016) "DCAF1 controls T-cell function via p53-dependent and -independent mechanisms." <i>Nat Commun</i> <b>7</b>:10307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728942 26728942]; doi: [https://dx.doi.org/10.1038/ncomms10307 10.1038/ncomms10307]; GPMDB: [http://gpmdb.org/data/keyword/26728942 120]. | #Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, (2016) "DCAF1 controls T-cell function via p53-dependent and -independent mechanisms." <i>Nat Commun</i> <b>7</b>:10307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728942 26728942]; doi: [https://dx.doi.org/10.1038/ncomms10307 10.1038/ncomms10307]; GPMDB: [http://gpmdb.org/data/keyword/26728942 120]. | ||
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#Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, (2016) "Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines." <i>PLoS One</i> <b>11</b>(4):e0154759; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27128805 27128805]; doi: [https://dx.doi.org/10.1371/journal.pone.0154759 10.1371/journal.pone.0154759]; GPMDB: [http://gpmdb.org/data/keyword/27128805 72]. | #Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, (2016) "Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines." <i>PLoS One</i> <b>11</b>(4):e0154759; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27128805 27128805]; doi: [https://dx.doi.org/10.1371/journal.pone.0154759 10.1371/journal.pone.0154759]; GPMDB: [http://gpmdb.org/data/keyword/27128805 72]. | ||
#Petrone A, Adamo ME, Cheng C, Kettenbach AN, (2016) "Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics." <i>Mol Cell Proteomics</i> <b>15</b>(7):2448–61; 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]. | #Petrone A, Adamo ME, Cheng C, Kettenbach AN, (2016) "Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics." <i>Mol Cell Proteomics</i> <b>15</b>(7):2448–61; 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]. | ||
+ | #Pozniak Y, Balint-Lahat N, Rudolph JD, Lindskog C, Katzir R, Avivi C, Pontén F, Ruppin E, Barshack I, Geiger T, (2016) "System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis." <i>Cell Syst</i> <b>2</b>(3):172–84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135363 27135363]; doi: [https://dx.doi.org/10.1016/j.cels.2016.02.001 10.1016/j.cels.2016.02.001]; GPMDB: [http://gpmdb.org/data/keyword/27135363 126]. | ||
#Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; 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]. | #Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; 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]. | ||
#Francavilla C, Papetti M, Rigbolt KT, Pedersen AK, Sigurdsson JO, Cazzamali G, Karemore G, Blagoev B, Olsen JV, (2016) "Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking." <i>Nat Struct Mol Biol</i> <b>23</b>(6):608–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27136326 27136326]; doi: [https://dx.doi.org/10.1038/nsmb.3218 10.1038/nsmb.3218]; GPMDB: [http://gpmdb.org/data/keyword/27136326 19]. | #Francavilla C, Papetti M, Rigbolt KT, Pedersen AK, Sigurdsson JO, Cazzamali G, Karemore G, Blagoev B, Olsen JV, (2016) "Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking." <i>Nat Struct Mol Biol</i> <b>23</b>(6):608–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27136326 27136326]; doi: [https://dx.doi.org/10.1038/nsmb.3218 10.1038/nsmb.3218]; GPMDB: [http://gpmdb.org/data/keyword/27136326 19]. | ||
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#Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i> <b>16</b>(13):1872–80; 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]. | #Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i> <b>16</b>(13):1872–80; 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) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <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]. | #Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <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]. | ||
- | #Arshid S, Tahir M, Fontes B, Montero EF, Castro MS, Sidoli S, Schwämmle V, Roepstorff P, Fontes W, ( | + | #Arshid S, Tahir M, Fontes B, Montero EF, Castro MS, Sidoli S, Schwämmle V, Roepstorff P, Fontes W, (2017) "Neutrophil proteomic analysis reveals the participation of antioxidant enzymes, motility and ribosomal proteins in the prevention of ischemic effects by preconditioning." <i>J Proteomics</i> <b>151</b>:162–173; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27208787 27208787]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.05.016 10.1016/j.jprot.2016.05.016]; GPMDB: [http://gpmdb.org/data/keyword/27208787 5]. |
#Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes." <i>Mol Cell Proteomics</i> <b>15</b>(8):2616–27; 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]. | #Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes." <i>Mol Cell Proteomics</i> <b>15</b>(8):2616–27; 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) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i> <b>34</b>(22):2583–90; 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]. | #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) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i> <b>34</b>(22):2583–90; 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]. | ||
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#Ahrné E, Glatter T, Viganò C, Schubert Cv, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i> <b>15</b>(8):2537–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 41]. | #Ahrné E, Glatter T, Viganò C, Schubert Cv, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i> <b>15</b>(8):2537–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 41]. | ||
#Chaubey PM, Hofstetter L, Roschitzki B, Stieger B, (2016) "Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver." <i>PLoS One</i> <b>11</b>(6):e0158033; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27347675 27347675]; doi: [https://dx.doi.org/10.1371/journal.pone.0158033 10.1371/journal.pone.0158033]; GPMDB: [http://gpmdb.org/data/keyword/27347675 60]. | #Chaubey PM, Hofstetter L, Roschitzki B, Stieger B, (2016) "Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver." <i>PLoS One</i> <b>11</b>(6):e0158033; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27347675 27347675]; doi: [https://dx.doi.org/10.1371/journal.pone.0158033 10.1371/journal.pone.0158033]; GPMDB: [http://gpmdb.org/data/keyword/27347675 60]. | ||
+ | #Bespyatykh J, Shitikov E, Butenko I, Altukhov I, Alexeev D, Mokrousov I, Dogonadze M, Zhuravlev V, Yablonsky P, Ilina E, Govorun V, (2016) "Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster." <i>Sci Rep</i> <b>6</b>:28985; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27356881 27356881]; doi: [https://dx.doi.org/10.1038/srep28985 10.1038/srep28985]; GPMDB: [http://gpmdb.org/data/keyword/27356881 23]. | ||
#Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT, (2016) "Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation." <i>Am J Physiol Cell Physiol</i> <b>311</b>(3):C404–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27357545 27357545]; doi: [https://dx.doi.org/10.1152/ajpcell.00121.2016 10.1152/ajpcell.00121.2016]; GPMDB: [http://gpmdb.org/data/keyword/27357545 3]. | #Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT, (2016) "Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation." <i>Am J Physiol Cell Physiol</i> <b>311</b>(3):C404–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27357545 27357545]; doi: [https://dx.doi.org/10.1152/ajpcell.00121.2016 10.1152/ajpcell.00121.2016]; GPMDB: [http://gpmdb.org/data/keyword/27357545 3]. | ||
#Dudekula K, Le Bihan T, (2016) "Data from quantitative label free proteomics analysis of rat spleen." <i>Data Brief</i> <b>8</b>:494–500; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27358910 27358910]; doi: [https://dx.doi.org/10.1016/j.dib.2016.05.058 10.1016/j.dib.2016.05.058]; GPMDB: [http://gpmdb.org/data/keyword/27358910 17]. | #Dudekula K, Le Bihan T, (2016) "Data from quantitative label free proteomics analysis of rat spleen." <i>Data Brief</i> <b>8</b>:494–500; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27358910 27358910]; doi: [https://dx.doi.org/10.1016/j.dib.2016.05.058 10.1016/j.dib.2016.05.058]; GPMDB: [http://gpmdb.org/data/keyword/27358910 17]. | ||
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#Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | #Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | ||
#Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I, (2016) "Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves." <i>J Proteome Res</i> <b>15</b>(12):4304–4317; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27643528 27643528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00348 10.1021/acs.jproteome.6b00348]; GPMDB: [http://gpmdb.org/data/keyword/27643528 28]. | #Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I, (2016) "Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves." <i>J Proteome Res</i> <b>15</b>(12):4304–4317; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27643528 27643528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00348 10.1021/acs.jproteome.6b00348]; GPMDB: [http://gpmdb.org/data/keyword/27643528 28]. | ||
- | #Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, ( | + | #Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2017) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i> <b>72</b>(1):115–127; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [http://gpmdb.org/data/keyword/27650186 42]. |
#Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-transcriptional Level." <i>Mol Cell Proteomics</i> <b>15</b>(11):3348–3360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. | #Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-transcriptional Level." <i>Mol Cell Proteomics</i> <b>15</b>(11):3348–3360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. | ||
#Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | #Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | ||
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#Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS, (2016) "In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis; presenting a comprehensive picture of pathways and processes affected by multiple sclerosis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27728768 27728768]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00659 10.1021/acs.jproteome.6b00659]; GPMDB: [http://gpmdb.org/data/keyword/27728768 26]. | #Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS, (2016) "In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis; presenting a comprehensive picture of pathways and processes affected by multiple sclerosis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27728768 27728768]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00659 10.1021/acs.jproteome.6b00659]; GPMDB: [http://gpmdb.org/data/keyword/27728768 26]. | ||
#Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium., Flicek P, Parkinson H, Clarke L, (2016) "The human-induced pluripotent stem cell initiative-data resources for cellular genetics." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27733501 27733501]; doi: [https://dx.doi.org/10.1093/nar/gkw928 10.1093/nar/gkw928]; GPMDB: [http://gpmdb.org/data/keyword/27733501 20]. | #Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium., Flicek P, Parkinson H, Clarke L, (2016) "The human-induced pluripotent stem cell initiative-data resources for cellular genetics." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27733501 27733501]; doi: [https://dx.doi.org/10.1093/nar/gkw928 10.1093/nar/gkw928]; GPMDB: [http://gpmdb.org/data/keyword/27733501 20]. | ||
- | #Kuzmanov U, Guo H, Buchsbaum D, Cosme J, Abbasi C, Isserlin R, Sharma P, Gramolini AO, Emili A, (2016) "Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(44):12592–12597; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27742792 27742792]; doi: [https://dx.doi.org/10.1073/pnas.1606444113 10.1073/pnas.1606444113]; GPMDB: [http://gpmdb.org/data/keyword/27742792 | + | #Kuzmanov U, Guo H, Buchsbaum D, Cosme J, Abbasi C, Isserlin R, Sharma P, Gramolini AO, Emili A, (2016) "Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(44):12592–12597; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27742792 27742792]; doi: [https://dx.doi.org/10.1073/pnas.1606444113 10.1073/pnas.1606444113]; GPMDB: [http://gpmdb.org/data/keyword/27742792 126]. |
#Sebé-Pedrós A, Peña MI, Capella-Gutiérrez S, Antó M, Gabaldón T, Ruiz-Trillo I, Sabidó E, (2016) "High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation." <i>Dev Cell</i> <b>39</b>(2):186–197; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27746046 27746046]; doi: [https://dx.doi.org/10.1016/j.devcel.2016.09.019 10.1016/j.devcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27746046 30]. | #Sebé-Pedrós A, Peña MI, Capella-Gutiérrez S, Antó M, Gabaldón T, Ruiz-Trillo I, Sabidó E, (2016) "High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation." <i>Dev Cell</i> <b>39</b>(2):186–197; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27746046 27746046]; doi: [https://dx.doi.org/10.1016/j.devcel.2016.09.019 10.1016/j.devcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27746046 30]. | ||
+ | #Varano M, Gaspari M, Quirino A, Cuda G, Liberto MC, Focà A, (2016) "Temperature-dependent regulation of the Ochrobactrum anthropi proteome." <i>Proteomics</i> <b>16</b>(23):3019–3024; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27753207 27753207]; doi: [https://dx.doi.org/10.1002/pmic.201600048 10.1002/pmic.201600048]; GPMDB: [http://gpmdb.org/data/keyword/27753207 12]. | ||
#Liljedahl L, Pedersen MH, Norlin J, McGuire JN, James P, (2016) "N-glycosylation proteome enrichment analysis in kidney reveals differences between diabetic mouse models." <i>Clin Proteomics</i> <b>13</b>:22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757071 27757071]; doi: [https://dx.doi.org/10.1186/s12014-016-9123-z 10.1186/s12014-016-9123-z]; GPMDB: [http://gpmdb.org/data/keyword/27757071 48]. | #Liljedahl L, Pedersen MH, Norlin J, McGuire JN, James P, (2016) "N-glycosylation proteome enrichment analysis in kidney reveals differences between diabetic mouse models." <i>Clin Proteomics</i> <b>13</b>:22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757071 27757071]; doi: [https://dx.doi.org/10.1186/s12014-016-9123-z 10.1186/s12014-016-9123-z]; GPMDB: [http://gpmdb.org/data/keyword/27757071 48]. | ||
#Zammit CM, Weiland F, Brugger J, Wade B, Winderbaum LJ, Nies DH, Southam G, Hoffmann P, Reith F, (2016) "Proteomic responses to gold(iii)-toxicity in the bacterium Cupriavidus metallidurans CH34." <i>Metallomics</i> <b>8</b>(11):1204–1216; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757465 27757465]; doi: [https://dx.doi.org/10.1039/c6mt00142d 10.1039/c6mt00142d]; GPMDB: [http://gpmdb.org/data/keyword/27757465 56]. | #Zammit CM, Weiland F, Brugger J, Wade B, Winderbaum LJ, Nies DH, Southam G, Hoffmann P, Reith F, (2016) "Proteomic responses to gold(iii)-toxicity in the bacterium Cupriavidus metallidurans CH34." <i>Metallomics</i> <b>8</b>(11):1204–1216; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757465 27757465]; doi: [https://dx.doi.org/10.1039/c6mt00142d 10.1039/c6mt00142d]; GPMDB: [http://gpmdb.org/data/keyword/27757465 56]. | ||
- | #Sialana FJ, Gulyassy P, Májek P, Sjöstedt E, Kis V, Müller AC, Rudashevskaya EL, Mulder J, Bennett KL, Lubec G, (2016) "Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels." <i>Proteomics</i> <b>16</b>(22):2911–2920; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27759936 27759936]; doi: [https://dx.doi.org/10.1002/pmic.201600234 10.1002/pmic.201600234]; GPMDB: [http://gpmdb.org/data/keyword/27759936 | + | #Sialana FJ, Gulyassy P, Májek P, Sjöstedt E, Kis V, Müller AC, Rudashevskaya EL, Mulder J, Bennett KL, Lubec G, (2016) "Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels." <i>Proteomics</i> <b>16</b>(22):2911–2920; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27759936 27759936]; doi: [https://dx.doi.org/10.1002/pmic.201600234 10.1002/pmic.201600234]; GPMDB: [http://gpmdb.org/data/keyword/27759936 86]. |
#Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | #Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | ||
- | #Assoni | + | #Assoni A, Coatti G, Valadares MC, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different Donors Mesenchymal Stromal Cells Secretomes Reveal Heterogeneous Profile of Relevance for Therapeutic Use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. |
+ | #Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 22]. | ||
#Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | #Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | ||
+ | #Cunsolo V, Fasoli E, Di Francesco A, Saletti R, Muccilli V, Gallina S, Righetti PG, Foti S, (2016) "Polyphemus, Odysseus and the ovine milk proteome." <i>J Proteomics</i> <b>152</b>:58–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27784645 27784645]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.007 10.1016/j.jprot.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27784645 40]. | ||
#Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | #Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | ||
#Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | #Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | ||
+ | #Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | ||
#Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i> <b>129</b>(24):4466–4479; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | #Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i> <b>129</b>(24):4466–4479; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | ||
#Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, Cowen LE, (2016) "Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity." <i>G3 (Bethesda)</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807047 27807047]; doi: [https://dx.doi.org/10.1534/g3.116.035675 10.1534/g3.116.035675]; GPMDB: [http://gpmdb.org/data/keyword/27807047 6]. | #Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, Cowen LE, (2016) "Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity." <i>G3 (Bethesda)</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807047 27807047]; doi: [https://dx.doi.org/10.1534/g3.116.035675 10.1534/g3.116.035675]; GPMDB: [http://gpmdb.org/data/keyword/27807047 6]. | ||
- | #Chen Y, Xie Y, Xu L, Zhan S, Xiao Y, Gao Y, Wu B, Ge W, ( | + | #Chen Y, Xie Y, Xu L, Zhan S, Xiao Y, Gao Y, Wu B, Ge W, (2017) "Protein content and functional characteristics of serum-purified exosomes from patients with colorectal cancer revealed by quantitative proteomics." <i>Int J Cancer</i> <b>140</b>(4):900–913; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27813080 27813080]; doi: [https://dx.doi.org/10.1002/ijc.30496 10.1002/ijc.30496]; GPMDB: [http://gpmdb.org/data/keyword/27813080 1]. |
- | #Kogel U, Titz B, Schlage WK, Nury C, Martin F, Oviedo A, Lebrun S, Elamin A, Guedj E, Trivedi K, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J, (2016) "Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke." <i>Regul Toxicol Pharmacol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818347 27818347]; doi: [https://dx.doi.org/10.1016/j.yrtph.2016.11.001 10.1016/j.yrtph.2016.11.001]; GPMDB: [http://gpmdb.org/data/keyword/27818347 | + | #Wang J, Mauvoisin D, Martin E, Atger F, Galindo AN, Dayon L, Sizzano F, Palini A, Kussmann M, Waridel P, Quadroni M, Dulić V, Naef F, Gachon F, (2016) "Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver." <i>Cell Metab</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818260 27818260]; doi: [https://dx.doi.org/10.1016/j.cmet.2016.10.003 10.1016/j.cmet.2016.10.003]; GPMDB: [http://gpmdb.org/data/keyword/27818260 19]. |
+ | #Kogel U, Titz B, Schlage WK, Nury C, Martin F, Oviedo A, Lebrun S, Elamin A, Guedj E, Trivedi K, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J, (2016) "Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke." <i>Regul Toxicol Pharmacol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818347 27818347]; doi: [https://dx.doi.org/10.1016/j.yrtph.2016.11.001 10.1016/j.yrtph.2016.11.001]; GPMDB: [http://gpmdb.org/data/keyword/27818347 36]. | ||
+ | #Schmitt K, Smolinski N, Neumann P, Schmaul S, Hofer-Pretz V, Braus GH, Valerius O, (2016) "Asc1p/RACK1 connects ribosomes to eukaryotic phospho-signaling." <i>Mol Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27821475 27821475]; doi: [https://dx.doi.org/10.1128/MCB.00279-16 10.1128/MCB.00279-16]; GPMDB: [http://gpmdb.org/data/keyword/27821475 274]. | ||
#Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR, (2016) "Multiparameter functional diversity of human C2H2 zinc finger proteins." <i>Genome Res</i> <b>26</b>(12):1742–1752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27852650 27852650]; doi: [https://dx.doi.org/10.1101/gr.209643.116 10.1101/gr.209643.116]; GPMDB: [http://gpmdb.org/data/keyword/27852650 224]. | #Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR, (2016) "Multiparameter functional diversity of human C2H2 zinc finger proteins." <i>Genome Res</i> <b>26</b>(12):1742–1752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27852650 27852650]; doi: [https://dx.doi.org/10.1101/gr.209643.116 10.1101/gr.209643.116]; GPMDB: [http://gpmdb.org/data/keyword/27852650 224]. | ||
#Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." <i>Nat Commun</i> <b>7</b>:13404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27869121 27869121]; doi: [https://dx.doi.org/10.1038/ncomms13404 10.1038/ncomms13404]; GPMDB: [http://gpmdb.org/data/keyword/27869121 138]. | #Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." <i>Nat Commun</i> <b>7</b>:13404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27869121 27869121]; doi: [https://dx.doi.org/10.1038/ncomms13404 10.1038/ncomms13404]; GPMDB: [http://gpmdb.org/data/keyword/27869121 138]. | ||
+ | #Wallace PW, Haernvall K, Ribitsch D, Zitzenbacher S, Schittmayer M, Steinkellner G, Gruber K, Guebitz GM, Birner-Gruenberger R, (2016) "PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes." <i>Appl Microbiol Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27872998 27872998]; doi: [https://dx.doi.org/10.1007/s00253-016-7992-8 10.1007/s00253-016-7992-8]; GPMDB: [http://gpmdb.org/data/keyword/27872998 28]. | ||
#St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. | #St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. | ||
#Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | #Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | ||
- | #Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." <i>Neuron</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27916455 27916455]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.10.064 10.1016/j.neuron.2016.10.064]; GPMDB: [http://gpmdb.org/data/keyword/27916455 | + | #Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." <i>Neuron</i> <b>92</b>(6):1220–1237; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27916455 27916455]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.10.064 10.1016/j.neuron.2016.10.064]; GPMDB: [http://gpmdb.org/data/keyword/27916455 377]. |
+ | #Tiberti N, Latham SL, Bush S, Cohen A, Opoka RO, John CC, Juillard A, Grau GE, Combes V, (2016) "Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content." <i>Sci Rep</i> <b>6</b>:37871; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27917875 27917875]; doi: [https://dx.doi.org/10.1038/srep37871 10.1038/srep37871]; GPMDB: [http://gpmdb.org/data/keyword/27917875 4]. | ||
+ | #Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27959563 27959563]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00834 10.1021/acs.jproteome.6b00834]; GPMDB: [http://gpmdb.org/data/keyword/27959563 4]. | ||
+ | #Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O, (2016) "ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27990823 27990823]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00881 10.1021/acs.jproteome.6b00881]; GPMDB: [http://gpmdb.org/data/keyword/27990823 12]. |
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 |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
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.
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.
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.
The following is a list of 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 December 25, 2016.