GPMDB Data Sources

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Revision as of 21:06, 27 March 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.

1 Current Public Data Sources
2 Previous Data Sources
3 Review process
4 Data from publications

Current Public Data Sources

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

ProteomeXchange/PRIDE;
MASSIVE;
PeptideAtlas/PASSEL;
ProteomicsDB;
The Chorus Project; and
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Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.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 March 5, 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." Proc Natl Acad Sci U S A 99(17):11049–54; PMID: 12177431; doi: 10.1073/pnas.172170199; GPMDB: 498.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ, (2007) "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer." Cell 131(6):1190–203; PMID: 18083107; doi: 10.1016/j.cell.2007.11.025; GPMDB: 104.
Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD, (2008) "Proteomics analysis of the causative agent of typhoid fever." J Proteome Res 7(2):546–57; PMID: 18166006; doi: 10.1021/pr070434u; GPMDB: 313.
Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ, (2008) "Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data." Anal Chem 80(4):961–71; PMID: 18189369; doi: 10.1021/ac701649e; GPMDB: 12.
Stevens SM Jr, Duncan RS, Koulen P, Prokai L, (2008) "Proteomic analysis of mouse brain microsomes: identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system." J Proteome Res 7(3):1046–54; PMID: 18271522; doi: 10.1021/pr7006279; GPMDB: 4.
Yocum AK, Gratsch TE, Leff N, Strahler JR, Hunter CL, Walker AK, Michailidis G, Omenn GS, O'Shea KS, Andrews PC, (2008) "Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation." Mol Cell Proteomics 7(4):750–67; PMID: 18304949; doi: 10.1074/mcp.M700399-MCP200; GPMDB: 18.
Lemeer S, Pinkse MW, Mohammed S, van Breukelen B, den Hertog J, Slijper M, Heck AJ, (2008) "Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo." J Proteome Res 7(4):1555–64; PMID: 18307296; doi: 10.1021/pr700667w; GPMDB: 148.
Zhai B, Villén J, Beausoleil SA, Mintseris J, Gygi SP, (2008) "Phosphoproteome analysis of Drosophila melanogaster embryos." J Proteome Res 7(4):1675–82; PMID: 18327897; doi: 10.1021/pr700696a; GPMDB: 24.
Denny P, Hagen FK, Hardt M, Liao L, Yan W, Arellanno M, Bassilian S, Bedi GS, Boontheung P, Cociorva D, Delahunty CM, Denny T, Dunsmore J, Faull KF, Gilligan J, Gonzalez-Begne M, Halgand F, Hall SC, Han X, Henson B, Hewel J, Hu S, Jeffrey S, Jiang J, Loo JA, Ogorzalek Loo RR, Malamud D, Melvin JE, Miroshnychenko O, Navazesh M, Niles R, Park SK, Prakobphol A, Ramachandran P, Richert M, Robinson S, Sondej M, Souda P, Sullivan MA, Takashima J, Than S, Wang J, Whitelegge JP, Witkowska HE, Wolinsky L, Xie Y, Xu T, Yu W, Ytterberg J, Wong DT, Yates JR 3rd, Fisher SJ, (2008) "The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions." J Proteome Res 7(5):1994–2006; PMID: 18361515; doi: 10.1021/pr700764j; GPMDB: 102.
Simó C, Bachi A, Cattaneo A, Guerrier L, Fortis F, Boschetti E, Podtelejnikov A, Righetti PG, (2008) "Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 1. Behavior of mono- to hexapeptides." Anal Chem 80(10):3547–56; PMID: 18399644; doi: 10.1021/ac702635v; GPMDB: 19.
Bachi A, Simó C, Restuccia U, Guerrier L, Fortis F, Boschetti E, Masseroli M, Righetti PG, (2008) "Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 2. Behavior of resins containing individual amino acids." Anal Chem 80(10):3557–65; PMID: 18410134; doi: 10.1021/ac8001353; GPMDB: 2.
Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S, (2008) "Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics." Science 320(5878):938–41; PMID: 18436743; doi: 10.1126/science.1157956; GPMDB: 28.
Ji H, Erfani N, Tauro BJ, Kapp EA, Zhu HJ, Moritz RL, Lim JW, Simpson RJ, (2008) "Difference gel electrophoresis analysis of Ras-transformed fibroblast cell-derived exosomes." Electrophoresis 29(12):2660–71; PMID: 18494037; doi: 10.1002/elps.200800015; GPMDB: 26.
Cao Z, Li C, Higginbotham JN, Franklin JL, Tabb DL, Graves-Deal R, Hill S, Cheek K, Jerome WG, Lapierre LA, Goldenring JR, Ham AJ, Coffey RJ, (2008) "Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis." Mol Cell Proteomics 7(9):1651–67; PMID: 18504258; doi: 10.1074/mcp.M700155-MCP200; GPMDB: 6.
Lemeer S, Jopling C, Gouw J, Mohammed S, Heck AJ, Slijper M, den Hertog J, (2008) "Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos." Mol Cell Proteomics 7(11):2176–87; PMID: 18550893; doi: 10.1074/mcp.M800081-MCP200; GPMDB: 31.
Sodek KL, Evangelou AI, Ignatchenko A, Agochiya M, Brown TJ, Ringuette MJ, Jurisica I, Kislinger T, (2008) "Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT)." Mol Biosyst 4(7):762–73; PMID: 18563251; doi: 10.1039/b717542f; GPMDB: 252.
Schimmel J, Larsen KM, Matic I, van Hagen M, Cox J, Mann M, Andersen JS, Vertegaal AC, (2008) "The ubiquitin-proteasome system is a key component of the SUMO-2/3 cycle." Mol Cell Proteomics 7(11):2107–22; PMID: 18565875; doi: 10.1074/mcp.M800025-MCP200; GPMDB: 5.
Yu MJ, Pisitkun T, Wang G, Aranda JF, Gonzales PA, Tchapyjnikov D, Shen RF, Alonso MA, Knepper MA, (2008) "Large-scale quantitative LC-MS/MS analysis of detergent-resistant membrane proteins from rat renal collecting duct." Am J Physiol Cell Physiol 295(3):C661–78; PMID: 18596208; doi: 10.1152/ajpcell.90650.2007; GPMDB: 137.
Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, Mootha VK, (2008) "A mitochondrial protein compendium elucidates complex I disease biology." Cell 134(1):112–23; PMID: 18614015; doi: 10.1016/j.cell.2008.06.016; GPMDB: 274.
Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ, (2008) "Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations." Genome Res 18(10):1660–9; PMID: 18653799; doi: 10.1101/gr.077644.108; GPMDB: 369.
Dix MM, Simon GM, Cravatt BF, (2008) "Global mapping of the topography and magnitude of proteolytic events in apoptosis." Cell 134(4):679–91; PMID: 18724940; doi: 10.1016/j.cell.2008.06.038; GPMDB: 178.
Kline KG, Frewen B, Bristow MR, Maccoss MJ, Wu CC, (2008) "High quality catalog of proteotypic peptides from human heart." J Proteome Res 7(11):5055–61; PMID: 18803417; doi: 10.1021/pr800239e; GPMDB: 96.
de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M, (2008) "Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast." Nature 455(7217):1251–4; PMID: 18820680; doi: 10.1038/nature07341; GPMDB: 505.
Liao L, Park SK, Xu T, Vanderklish P, Yates JR 3rd, (2008) "Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice." Proc Natl Acad Sci U S A 105(40):15281–6; PMID: 18829439; doi: 10.1073/pnas.0804678105; GPMDB: 15.
Lin MK, Lee YJ, Lough TJ, Phinney BS, Lucas WJ, (2009) "Analysis of the pumpkin phloem proteome provides insights into angiosperm sieve tube function." Mol Cell Proteomics 8(2):343–56; PMID: 18936055; doi: 10.1074/mcp.M800420-MCP200; GPMDB: 346.
Slebos RJ, Brock JW, Winters NF, Stuart SR, Martinez MA, Li M, Chambers MC, Zimmerman LJ, Ham AJ, Tabb DL, Liebler DC, (2008) "Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry." J Proteome Res 7(12):5286–94; PMID: 18939861; doi: 10.1021/pr8004666; GPMDB: 346.
Mittler G, Butter F, Mann M, (2009) "A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements." Genome Res 19(2):284–93; PMID: 19015324; doi: 10.1101/gr.081711.108; GPMDB: 7.
Codreanu SG, Zhang B, Sobecki SM, Billheimer DD, Liebler DC, (2009) "Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal." Mol Cell Proteomics 8(4):670–80; PMID: 19054759; doi: 10.1074/mcp.M800070-MCP200; GPMDB: 168.
Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI, (2009) "Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification." J Proteome Res 8(2):887–99; PMID: 19072539; doi: 10.1021/pr800535h; GPMDB: 18.
Du J, Bernasconi P, Clauser KR, Mani DR, Finn SP, Beroukhim R, Burns M, Julian B, Peng XP, Hieronymus H, Maglathlin RL, Lewis TA, Liau LM, Nghiemphu P, Mellinghoff IK, Louis DN, Loda M, Carr SA, Kung AL, Golub TR, (2009) "Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy." Nat Biotechnol 27(1):77–83; PMID: 19098899; doi: 10.1038/nbt.1513; GPMDB: 36.
Glatter T, Wepf A, Aebersold R, Gstaiger M, (2009) "An integrated workflow for charting the human interaction proteome: insights into the PP2A system." Mol Syst Biol 5:237; PMID: 19156129; doi: 10.1038/msb.2008.75; GPMDB: 62.
Bivi N, Bereszczak JZ, Romanello M, Zeef LA, Delneri D, Quadrifoglio F, Moro L, Brancia FL, Tell G, (2009) "Transcriptome and proteome analysis of osteocytes treated with nitrogen-containing bisphosphonates." J Proteome Res 8(3):1131–42; PMID: 19226166; doi: 10.1021/pr8005606; GPMDB: 10.
Pieper R, Huang ST, Clark DJ, Robinson JM, Alami H, Parmar PP, Suh MJ, Kuntumalla S, Bunai CL, Perry RD, Fleischmann RD, Peterson SN, (2009) "Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes." Proteome Sci 7:5; PMID: 19228400; doi: 10.1186/1477-5956-7-5; GPMDB: 376.
de Sousa Abreu R, Sanchez-Diaz PC, Vogel C, Burns SC, Ko D, Burton TL, Vo DT, Chennasamudaram S, Le SY, Shapiro BA, Penalva LO, (2009) "Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes." J Biol Chem 284(18):12125–35; PMID: 19258308; doi: 10.1074/jbc.M809605200; GPMDB: 14.
Mathias RA, Wang B, Ji H, Kapp EA, Moritz RL, Zhu HJ, Simpson RJ, (2009) "Secretome-based proteomic profiling of Ras-transformed MDCK cells reveals extracellular modulators of epithelial-mesenchymal transition." J Proteome Res 8(6):2827–37; PMID: 19296674; doi: 10.1021/pr8010974; GPMDB: 98.
Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ, (2009) "Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics." Nat Protoc 4(4):484–94; PMID: 19300442; doi: 10.1038/nprot.2009.21; GPMDB: 3.
Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R, (2009) "Integrating shotgun proteomics and mRNA expression data to improve protein identification." Bioinformatics 25(11):1397–403; PMID: 19318424; doi: 10.1093/bioinformatics/btp168; GPMDB: 8.
Rudomin EL, Carr SA, Jaffe JD, (2009) "Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx)." J Proteome Res 8(6):3154–60; PMID: 19344186; doi: 10.1021/pr801017a; GPMDB: 11.
Steiling K, Kadar AY, Bergerat A, Flanigon J, Sridhar S, Shah V, Ahmad QR, Brody JS, Lenburg ME, Steffen M, Spira A, (2009) "Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokers." PLoS One 4(4):e5043; PMID: 19357784; doi: 10.1371/journal.pone.0005043; GPMDB: 589.
Hjelmervik TO, Jonsson R, Bolstad AI, (2009) "The minor salivary gland proteome in Sjögren's syndrome." Oral Dis 15(5):342–53; PMID: 19364392; doi: 10.1111/j.1601-0825.2009.01531.x; GPMDB: 2.
Zanivan S, Gnad F, Wickström SA, Geiger T, Macek B, Cox J, Fässler R, Mann M, (2008) "Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry." J Proteome Res 7(12):5314–26; PMID: 19367708; GPMDB: 20.
Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S, (2009) "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Plant Physiol 150(2):889–903; PMID: 19376835; doi: 10.1104/pp.109.138677; GPMDB: 13.
Parker KC, Walsh RJ, Salajegheh M, Amato AA, Krastins B, Sarracino DA, Greenberg SA, (2009) "Characterization of human skeletal muscle biopsy samples using shotgun proteomics." J Proteome Res 8(7):3265–77; PMID: 19382779; doi: 10.1021/pr800873q; GPMDB: 36.
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group, (2009) "A HUPO test sample study reveals common problems in mass spectrometry-based proteomics." Nat Methods 6(6):423–30; PMID: 19448641; doi: 10.1038/nmeth.1333; GPMDB: 14.
Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS, Grant SG, (2009) "Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins." Mol Syst Biol 5:269; PMID: 19455133; doi: 10.1038/msb.2009.27; GPMDB: 70.
Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC, (2009) "Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis." Mol Cell Proteomics 8(8):1988–98; PMID: 19467989; doi: 10.1074/mcp.M800518-MCP200; GPMDB: 230.
Burkard ME, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery DM, Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV, (2009) "Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells." PLoS Biol 7(5):e1000111; PMID: 19468302; doi: 10.1371/journal.pbio.1000111; GPMDB: 1.
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Gielisch I, Hardt C, Wittig I, Meierhofer D, (2016) "An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters." Mol Cell Proteomics; PMID: 26852163; doi: 10.1074/mcp.M115.053181; GPMDB: 60.
Peffers MJ, Collins J, Fang Y, Goljanek-Whysall K, Rushton M, Loughlin J, Proctor C, Clegg PD, (2016) "Age-related changes in mesenchymal stem cells identified using a multi-omics approach." Eur Cell Mater 31:136–59; PMID: 26853623; GPMDB: 8.
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) "Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers." Sci Rep 6:21507; PMID: 26857143; doi: 10.1038/srep21507; GPMDB: 9.
Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C, (2016) "Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes." Proc Natl Acad Sci U S A 113(8):E968–77; PMID: 26858453; doi: 10.1073/pnas.1521230113; GPMDB: 56.
Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." Sci Signal 9(414):ra15; PMID: 26861043; doi: 10.1126/scisignal.aac5820; GPMDB: 76.
Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The endoplasmic reticulum chaperone calnexin is a NADPH oxidase Nox4 interacting protein." J Biol Chem; PMID: 26861875; doi: 10.1074/jbc.M115.710772; GPMDB: 80.
Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." J Proteomics 136:55–67; PMID: 26873878; doi: 10.1016/j.jprot.2016.02.002; GPMDB: 9.
Knöppel A, Näsvall J, Andersson DI, (2016) "Compensating the Fitness Costs of Synonymous Mutations." Mol Biol Evol; PMID: 26882986; doi: 10.1093/molbev/msw028; GPMDB: 72.
Creedon H, Gómez-Cuadrado L, Tarnauskaitė Ž, 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) "Identification of novel pathways linking epithelial-to-mesenchymal transition with resistance to HER2-targeted therapy." Oncotarget; PMID: 26883193; doi: 10.18632/oncotarget.7317; GPMDB: 6.
Zufferey A, Ibberson M, Reny JL, Nolli S, Schvartz D, Docquier M, Xenarios I, Sanchez JC, Fontana P, (2016) "New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach." Hum Genet 135(4):403–14; PMID: 26883867; doi: 10.1007/s00439-016-1642-1; GPMDB: 13.
Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T, (2016) "Deubiquitylation of protein cargo is not an essential step in exosome formation." Mol Cell Proteomics; PMID: 26884507; doi: 10.1074/mcp.M115.054965; GPMDB: 64.
Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, Wang KY, Lin SY, Shih YL, (2016) "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane." Mol Cell Proteomics; PMID: 26889046; doi: 10.1074/mcp.M115.053603; GPMDB: 4.
Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE, (2016) "Proteomic analysis reveals branch-specific regulation of the unfolded protein response by nonsense-mediated mRNA decay." Mol Cell Proteomics; PMID: 26896796; doi: 10.1074/mcp.M115.054056; GPMDB: 4.
Zilkenat S, Franz-Wachtel M, Stierhof YD, Galan JE, Macek B, Wagner S, (2016) "Determination of the stoichiometry of the complete bacterial type III secretion needle complex using a combined quantitative proteomic approach." Mol Cell Proteomics; PMID: 26900162; doi: 10.1074/mcp.M115.056598; GPMDB: 18.
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) "Integrative subcellular proteomic analysis allows accurate prediction of human disease causing genes." Genome Res; PMID: 26912414; doi: 10.1101/gr.198911.115; GPMDB: 26.
Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M, (2016) "In vivo interaction proteomics in C. elegans embryos provides new insights into P granule dynamics." Mol Cell Proteomics; PMID: 26912668; doi: 10.1074/mcp.M115.053975; GPMDB: 66.
Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M, (2016) "New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants." J Proteomics 138:1–19; PMID: 26915584; doi: 10.1016/j.jprot.2016.02.012; GPMDB: 24.
de Torre-Minguela C, Barberà-Cremades M, Gómez AI, Martín-Sánchez F, Pelegrín P, (2016) "Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process." Sci Rep 6:22586; PMID: 26935289; doi: 10.1038/srep22586; GPMDB: 118.
Salih M, Demmers JA, Bezstarosti K, Leonhard WN, Losekoot M, van Kooten C, Gansevoort RT, Peters DJ, Zietse R, Hoorn EJ, DIPAK Consortium, (2016) "Proteomics of Urinary Vesicles Links Plakins and Complement to Polycystic Kidney Disease." J Am Soc Nephrol; PMID: 26940098; doi: 10.1681/ASN.2015090994; GPMDB: 7.
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) "Natural genetic variation differentially affects the proteome and transcriptome in C. elegans." Mol Cell Proteomics; PMID: 26944343; doi: 10.1074/mcp.M115.052548; GPMDB: 12.
Xin L, Xu B, Ma L, Hou Q, Ye M, Meng S, Ding X, Ge W, (2016) "Proteomics study reveals that the dysregulation of focal adhesion and ribosome contribute to early pregnancy loss." Proteomics Clin Appl; PMID: 26947931; doi: 10.1002/prca.201500136; GPMDB: 1.
Adewole OO, Erhabor GE, Adewole TO, Ojo AO, Harriet O, Wolfe LM, Prenni JE, (2016) "Proteomic profiling of Eccrine sweat reveals its potential as a diagnostic biofluid for active tuberculosis." Proteomics Clin Appl; PMID: 26948146; doi: 10.1002/prca.201500071; GPMDB: 10.
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) "Characterization of various cell lines from different ampullary cancer subtypes and cancer associated fibroblast-mediated responses." BMC Cancer 16(1):195; PMID: 26951071; doi: 10.1186/s12885-016-2193-5; GPMDB: 5.
Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." Int J Med Microbiol; PMID: 26996810; doi: 10.1016/j.ijmm.2016.02.004; GPMDB: 300.
Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher D, Coon JJ, (2016) "The peripheral blood eosinophil proteome." J Proteome Res; PMID: 27005946; doi: 10.1021/acs.jproteome.6b00006; GPMDB: 24.

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@@ Line 28: / Line 28: @@
 #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) &quot;Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.&quot; <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049&ndash;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].
 #Liu T, Qian WJ, Strittmatter EF, Camp DG 2nd, Anderson GA, Thrall BD, Smith RD,  (2004) &quot;High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology.&quot; <i>Anal Chem</i> <b>76</b>(18):5345&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [http://gpmdb.org/data/keyword/15362891 6].
-#Sauer G, KÃ¶rner R, Hanisch A, Ries A, Nigg EA, SilljÃ© HH,  (2005) &quot;Proteome analysis of the human mitotic spindle.&quot; <i>Mol Cell Proteomics</i> <b>4</b>(1):35&ndash;43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15561729 15561729]; doi: [https://dx.doi.org/10.1074/mcp.M400158-MCP200 10.1074/mcp.M400158-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/15561729 1].
+#Sauer G, Körner R, Hanisch A, Ries A, Nigg EA, Silljé HH,  (2005) &quot;Proteome analysis of the human mitotic spindle.&quot; <i>Mol Cell Proteomics</i> <b>4</b>(1):35&ndash;43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15561729 15561729]; doi: [https://dx.doi.org/10.1074/mcp.M400158-MCP200 10.1074/mcp.M400158-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/15561729 1].
 #Klein C, Garcia-Rizo C, Bisle B, Scheffer B, Zischka H, Pfeiffer F, Siedler F, Oesterhelt D,  (2005) &quot;The membrane proteome of Halobacterium salinarum.&quot; <i>Proteomics</i> <b>5</b>(1):180&ndash;97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15619294 15619294]; doi: [https://dx.doi.org/10.1002/pmic.200400943 10.1002/pmic.200400943]; GPMDB: [http://gpmdb.org/data/keyword/15619294 37].
 #Searle BC, Dasari S, Wilmarth PA, Turner M, Reddy AP, David LL, Nagalla SR,  (2005) &quot;Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm.&quot; <i>J Proteome Res</i> <b>4</b>(2):546&ndash;54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15822933 15822933]; doi: [https://dx.doi.org/10.1021/pr049781j 10.1021/pr049781j]; GPMDB: [http://gpmdb.org/data/keyword/15822933 4].
@@ Line 36: / Line 36: @@
 #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) &quot;Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype.&quot; <i>J Proteome Res</i> <b>5</b>(5):1143&ndash;54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16674103 16674103]; doi: [https://dx.doi.org/10.1021/pr050455t 10.1021/pr050455t]; GPMDB: [http://gpmdb.org/data/keyword/16674103 3].
 #Bisle B, Schmidt A, Scheibe B, Klein C, Tebbe A, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D,  (2006) &quot;Quantitative profiling of the membrane proteome in a halophilic archaeon.&quot; <i>Mol Cell Proteomics</i> <b>5</b>(9):1543&ndash;58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16804162 16804162]; doi: [https://dx.doi.org/10.1074/mcp.M600106-MCP200 10.1074/mcp.M600106-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/16804162 32].
-#Hamacher M, Apweiler R, Arnold G, Becker A, BlÃ¼ggel M, Carrette O, Colvis C, Dunn MJ, FrÃ¶hlich 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, StÃ¼hler 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) &quot;HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.&quot; <i>Proteomics</i> <b>6</b>(18):4890&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16927433 16927433]; doi: [https://dx.doi.org/10.1002/pmic.200600295 10.1002/pmic.200600295]; GPMDB: [http://gpmdb.org/data/keyword/16927433 296].
+#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) &quot;HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.&quot; <i>Proteomics</i> <b>6</b>(18):4890&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16927433 16927433]; doi: [https://dx.doi.org/10.1002/pmic.200600295 10.1002/pmic.200600295]; GPMDB: [http://gpmdb.org/data/keyword/16927433 296].
-#Beausoleil SA, VillÃ©n J, Gerber SA, Rush J, Gygi SP,  (2006) &quot;A probability-based approach for high-throughput protein phosphorylation analysis and site localization.&quot; <i>Nat Biotechnol</i> <b>24</b>(10):1285&ndash;92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16964243 16964243]; doi: [https://dx.doi.org/10.1038/nbt1240 10.1038/nbt1240]; GPMDB: [http://gpmdb.org/data/keyword/16964243 31].
+#Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP,  (2006) &quot;A probability-based approach for high-throughput protein phosphorylation analysis and site localization.&quot; <i>Nat Biotechnol</i> <b>24</b>(10):1285&ndash;92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16964243 16964243]; doi: [https://dx.doi.org/10.1038/nbt1240 10.1038/nbt1240]; GPMDB: [http://gpmdb.org/data/keyword/16964243 31].
 #Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS,  (2006) &quot;An integrated systems approach for understanding cellular responses to gamma radiation.&quot; <i>Mol Syst Biol</i> <b>2</b>:47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16969339 16969339]; doi: [https://dx.doi.org/10.1038/msb4100091 10.1038/msb4100091]; GPMDB: [http://gpmdb.org/data/keyword/16969339 27].
 #Price TS, Lucitt MB, Wu W, Austin DJ, Pizarro A, Yocum AK, Blair IA, FitzGerald GA, Grosser T,  (2007) &quot;EBP, a program for protein identification using multiple tandem mass spectrometry datasets.&quot; <i>Mol Cell Proteomics</i> <b>6</b>(3):527&ndash;36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17164401 17164401]; doi: [https://dx.doi.org/10.1074/mcp.T600049-MCP200 10.1074/mcp.T600049-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/17164401 314].
-#Tanner S, Shen Z, Ng J, Florea L, GuigÃ³ R, Briggs SP, Bafna V,  (2007) &quot;Improving gene annotation using peptide mass spectrometry.&quot; <i>Genome Res</i> <b>17</b>(2):231&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17189379 17189379]; doi: [https://dx.doi.org/10.1101/gr.5646507 10.1101/gr.5646507]; GPMDB: [http://gpmdb.org/data/keyword/17189379 1].
+#Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V,  (2007) &quot;Improving gene annotation using peptide mass spectrometry.&quot; <i>Genome Res</i> <b>17</b>(2):231&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17189379 17189379]; doi: [https://dx.doi.org/10.1101/gr.5646507 10.1101/gr.5646507]; GPMDB: [http://gpmdb.org/data/keyword/17189379 1].
 #Konstantinidis K, Tebbe A, Klein C, Scheffer B, Aivaliotis M, Bisle B, Falb M, Pfeiffer F, Siedler F, Oesterhelt D,  (2007) &quot;Genome-wide proteomics of Natronomonas pharaonis.&quot; <i>J Proteome Res</i> <b>6</b>(1):185&ndash;93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17203963 17203963]; doi: [https://dx.doi.org/10.1021/pr060352q 10.1021/pr060352q]; GPMDB: [http://gpmdb.org/data/keyword/17203963 176].
-#VillÃ©n J, Beausoleil SA, Gerber SA, Gygi SP,  (2007) &quot;Large-scale phosphorylation analysis of mouse liver.&quot; <i>Proc Natl Acad Sci U S A</i> <b>104</b>(5):1488&ndash;93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17242355 17242355]; doi: [https://dx.doi.org/10.1073/pnas.0609836104 10.1073/pnas.0609836104]; GPMDB: [http://gpmdb.org/data/keyword/17242355 1].
+#Villén J, Beausoleil SA, Gerber SA, Gygi SP,  (2007) &quot;Large-scale phosphorylation analysis of mouse liver.&quot; <i>Proc Natl Acad Sci U S A</i> <b>104</b>(5):1488&ndash;93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17242355 17242355]; doi: [https://dx.doi.org/10.1073/pnas.0609836104 10.1073/pnas.0609836104]; GPMDB: [http://gpmdb.org/data/keyword/17242355 1].
 #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) &quot;The low molecular weight proteome of Halobacterium salinarum.&quot; <i>J Proteome Res</i> <b>6</b>(4):1510&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17326674 17326674]; doi: [https://dx.doi.org/10.1021/pr060634q 10.1021/pr060634q]; GPMDB: [http://gpmdb.org/data/keyword/17326674 10].
 #Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC,  (2007) &quot;Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.&quot; <i>Science</i> <b>316</b>(5822):280&ndash;5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17431180 17431180]; doi: [https://dx.doi.org/10.1126/science.1137614 10.1126/science.1137614]; GPMDB: [http://gpmdb.org/data/keyword/17431180 2].
@@ Line 58: / Line 58: @@
 #Yocum AK, Gratsch TE, Leff N, Strahler JR, Hunter CL, Walker AK, Michailidis G, Omenn GS, O'Shea KS, Andrews PC,  (2008) &quot;Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation.&quot; <i>Mol Cell Proteomics</i> <b>7</b>(4):750&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18304949 18304949]; doi: [https://dx.doi.org/10.1074/mcp.M700399-MCP200 10.1074/mcp.M700399-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/18304949 18].
 #Lemeer S, Pinkse MW, Mohammed S, van Breukelen B, den Hertog J, Slijper M, Heck AJ,  (2008) &quot;Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo.&quot; <i>J Proteome Res</i> <b>7</b>(4):1555&ndash;64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18307296 18307296]; doi: [https://dx.doi.org/10.1021/pr700667w 10.1021/pr700667w]; GPMDB: [http://gpmdb.org/data/keyword/18307296 148].
-#Zhai B, VillÃ©n J, Beausoleil SA, Mintseris J, Gygi SP,  (2008) &quot;Phosphoproteome analysis of Drosophila melanogaster embryos.&quot; <i>J Proteome Res</i> <b>7</b>(4):1675&ndash;82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18327897 18327897]; doi: [https://dx.doi.org/10.1021/pr700696a 10.1021/pr700696a]; GPMDB: [http://gpmdb.org/data/keyword/18327897 24].
+#Zhai B, Villén J, Beausoleil SA, Mintseris J, Gygi SP,  (2008) &quot;Phosphoproteome analysis of Drosophila melanogaster embryos.&quot; <i>J Proteome Res</i> <b>7</b>(4):1675&ndash;82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18327897 18327897]; doi: [https://dx.doi.org/10.1021/pr700696a 10.1021/pr700696a]; GPMDB: [http://gpmdb.org/data/keyword/18327897 24].
 #Denny P, Hagen FK, Hardt M, Liao L, Yan W, Arellanno M, Bassilian S, Bedi GS, Boontheung P, Cociorva D, Delahunty CM, Denny T, Dunsmore J, Faull KF, Gilligan J, Gonzalez-Begne M, Halgand F, Hall SC, Han X, Henson B, Hewel J, Hu S, Jeffrey S, Jiang J, Loo JA, Ogorzalek Loo RR, Malamud D, Melvin JE, Miroshnychenko O, Navazesh M, Niles R, Park SK, Prakobphol A, Ramachandran P, Richert M, Robinson S, Sondej M, Souda P, Sullivan MA, Takashima J, Than S, Wang J, Whitelegge JP, Witkowska HE, Wolinsky L, Xie Y, Xu T, Yu W, Ytterberg J, Wong DT, Yates JR 3rd, Fisher SJ,  (2008) &quot;The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions.&quot; <i>J Proteome Res</i> <b>7</b>(5):1994&ndash;2006; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18361515 18361515]; doi: [https://dx.doi.org/10.1021/pr700764j 10.1021/pr700764j]; GPMDB: [http://gpmdb.org/data/keyword/18361515 102].
-#SimÃ³ C, Bachi A, Cattaneo A, Guerrier L, Fortis F, Boschetti E, Podtelejnikov A, Righetti PG,  (2008) &quot;Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 1. Behavior of mono- to hexapeptides.&quot; <i>Anal Chem</i> <b>80</b>(10):3547&ndash;56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18399644 18399644]; doi: [https://dx.doi.org/10.1021/ac702635v 10.1021/ac702635v]; GPMDB: [http://gpmdb.org/data/keyword/18399644 19].
+#Simó C, Bachi A, Cattaneo A, Guerrier L, Fortis F, Boschetti E, Podtelejnikov A, Righetti PG,  (2008) &quot;Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 1. Behavior of mono- to hexapeptides.&quot; <i>Anal Chem</i> <b>80</b>(10):3547&ndash;56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18399644 18399644]; doi: [https://dx.doi.org/10.1021/ac702635v 10.1021/ac702635v]; GPMDB: [http://gpmdb.org/data/keyword/18399644 19].
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@@ Line 90: / Line 90: @@
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+#Hjelmervik TO, Jonsson R, Bolstad AI,  (2009) &quot;The minor salivary gland proteome in Sjögren's syndrome.&quot; <i>Oral Dis</i> <b>15</b>(5):342&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19364392 19364392]; doi: [https://dx.doi.org/10.1111/j.1601-0825.2009.01531.x 10.1111/j.1601-0825.2009.01531.x]; GPMDB: [http://gpmdb.org/data/keyword/19364392 2].
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+#Zanivan S, Gnad F, Wickström SA, Geiger T, Macek B, Cox J, Fässler R, Mann M,  (2008) &quot;Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry.&quot; <i>J Proteome Res</i> <b>7</b>(12):5314&ndash;26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19367708 19367708]; GPMDB: [http://gpmdb.org/data/keyword/19367708 20].
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+#Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS, Grant SG,  (2009) &quot;Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins.&quot; <i>Mol Syst Biol</i> <b>5</b>:269; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19455133 19455133]; doi: [https://dx.doi.org/10.1038/msb.2009.27 10.1038/msb.2009.27]; GPMDB: [http://gpmdb.org/data/keyword/19455133 70].
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+#Ozlü N, Monigatti F, Renard BY, Field CM, Steen H, Mitchison TJ, Steen JJ,  (2010) &quot;Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition.&quot; <i>Mol Cell Proteomics</i> <b>9</b>(2):336&ndash;50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19786723 19786723]; doi: [https://dx.doi.org/10.1074/mcp.M900308-MCP200 10.1074/mcp.M900308-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/19786723 13].
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@@ Line 119: / Line 119: @@
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+#Baudet M, Ortet P, Gaillard JC, Fernandez B, Guérin P, Enjalbal C, Subra G, de Groot A, Barakat M, Dedieu A, Armengaud J,  (2010) &quot;Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.&quot; <i>Mol Cell Proteomics</i> <b>9</b>(2):415&ndash;26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19875382 19875382]; doi: [https://dx.doi.org/10.1074/mcp.M900359-MCP200 10.1074/mcp.M900359-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/19875382 19].
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+#Pitteri SJ, JeBailey L, Faça VM, Thorpe JD, Silva MA, Ireton RC, Horton MB, Wang H, Pruitt LC, Zhang Q, Cheng KH, Urban N, Hanash SM, Dinulescu DM,  (2009) &quot;Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.&quot; <i>PLoS One</i> <b>4</b>(11):e7916; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19936259 19936259]; doi: [https://dx.doi.org/10.1371/journal.pone.0007916 10.1371/journal.pone.0007916]; GPMDB: [http://gpmdb.org/data/keyword/19936259 144].
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@@ Line 134: / Line 134: @@
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@@ Line 144: / Line 144: @@
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@@ Line 172: / Line 172: @@
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+#Impens F, Colaert N, Helsens K, Ghesquière B, Timmerman E, De Bock PJ, Chain BM, Vandekerckhove J, Gevaert K,  (2010) &quot;A quantitative proteomics design for systematic identification of protease cleavage events.&quot; <i>Mol Cell Proteomics</i> <b>9</b>(10):2327&ndash;33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20627866 20627866]; doi: [https://dx.doi.org/10.1074/mcp.M110.001271 10.1074/mcp.M110.001271]; GPMDB: [http://gpmdb.org/data/keyword/20627866 3].
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+#Mäusbacher N, Schreiber TB, Daub H,  (2010) &quot;Glycoprotein capture and quantitative phosphoproteomics indicate coordinated regulation of cell migration upon lysophosphatidic acid stimulation.&quot; <i>Mol Cell Proteomics</i> <b>9</b>(11):2337&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/20639409 20639409]; doi: [https://dx.doi.org/10.1074/mcp.M110.000737 10.1074/mcp.M110.000737]; GPMDB: [http://gpmdb.org/data/keyword/20639409 70].
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@@ Line 197: / Line 197: @@
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-#de Souza GA, Arntzen MÃ˜, Fortuin S, SchÃ¼rch AC, MÃ¥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].
+#de Souza GA, Arntzen MØ, Fortuin S, Schürch AC, Målen 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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@@ Line 208: / Line 208: @@
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+#Skirycz A, Memmi S, De Bodt S, Maleux K, Obata T, Fernie AR, Devreese B, Inzé 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, Boström AK, Impens F, Fredlund E, Van Peer G, De Antonellis P, von Stedingk K, Ghesquière 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-β 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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+#Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén 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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+#Bantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, Dümpelfeld 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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@@ Line 239: / Line 239: @@
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+#Gfeller A, Baerenfaller K, Loscos J, Chételat A, Baginsky S, Farmer EE,  (2011) &quot;Jasmonate controls polypeptide patterning in undamaged tissue in wounded Arabidopsis leaves.&quot; <i>Plant Physiol</i> <b>156</b>(4):1797&ndash;807; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21693672 21693672]; doi: [https://dx.doi.org/10.1104/pp.111.181008 10.1104/pp.111.181008]; GPMDB: [http://gpmdb.org/data/keyword/21693672 8].
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-#Ã˜stergaard L, HonorÃ© B, Thorsen LB, Baandrup J, Eskildsen-Helmond Y, Laursen BE, Vorum H, Mulvany MJ, Simonsen U,  (2011) &quot;Pulmonary pressure reduction attenuates expression of proteins identified by lung proteomic profiling in pulmonary hypertensive rats.&quot; <i>Proteomics</i> <b>11</b>(23):4492&ndash;502; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21905223 21905223]; doi: [https://dx.doi.org/10.1002/pmic.201100171 10.1002/pmic.201100171]; GPMDB: [http://gpmdb.org/data/keyword/21905223 1].
+#Østergaard L, Honoré B, Thorsen LB, Baandrup J, Eskildsen-Helmond Y, Laursen BE, Vorum H, Mulvany MJ, Simonsen U,  (2011) &quot;Pulmonary pressure reduction attenuates expression of proteins identified by lung proteomic profiling in pulmonary hypertensive rats.&quot; <i>Proteomics</i> <b>11</b>(23):4492&ndash;502; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21905223 21905223]; doi: [https://dx.doi.org/10.1002/pmic.201100171 10.1002/pmic.201100171]; GPMDB: [http://gpmdb.org/data/keyword/21905223 1].
 #Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP,  (2011) &quot;Systematic and quantitative assessment of the ubiquitin-modified proteome.&quot; <i>Mol Cell</i> <b>44</b>(2):325&ndash;40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21906983 21906983]; doi: [https://dx.doi.org/10.1016/j.molcel.2011.08.025 10.1016/j.molcel.2011.08.025]; GPMDB: [http://gpmdb.org/data/keyword/21906983 90].
-#Nguyen HM, Baudet M, CuinÃ© S, Adriano JM, Barthe D, Billon E, Bruley C, Beisson F, Peltier G, Ferro M, Li-Beisson Y,  (2011) &quot;Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: with focus on proteins involved in lipid metabolism.&quot; <i>Proteomics</i> <b>11</b>(21):4266&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21928291 21928291]; doi: [https://dx.doi.org/10.1002/pmic.201100114 10.1002/pmic.201100114]; GPMDB: [http://gpmdb.org/data/keyword/21928291 1].
+#Nguyen HM, Baudet M, Cuiné S, Adriano JM, Barthe D, Billon E, Bruley C, Beisson F, Peltier G, Ferro M, Li-Beisson Y,  (2011) &quot;Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: with focus on proteins involved in lipid metabolism.&quot; <i>Proteomics</i> <b>11</b>(21):4266&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21928291 21928291]; doi: [https://dx.doi.org/10.1002/pmic.201100114 10.1002/pmic.201100114]; GPMDB: [http://gpmdb.org/data/keyword/21928291 1].
 #Rogers LD, Brown NF, Fang Y, Pelech S, Foster LJ,  (2011) &quot;Phosphoproteomic analysis of Salmonella-infected cells identifies key kinase regulators and SopB-dependent host phosphorylation events.&quot; <i>Sci Signal</i> <b>4</b>(191):rs9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21934108 21934108]; doi: [https://dx.doi.org/10.1126/scisignal.2001668 10.1126/scisignal.2001668]; GPMDB: [http://gpmdb.org/data/keyword/21934108 9].
-#Boisvert FM, Ahmad Y, GierliÅ„ski M, CharriÃ¨re F, Lamont D, Scott M, Barton G, Lamond AI,  (2012) &quot;A quantitative spatial proteomics analysis of proteome turnover in human cells.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):M111.011429; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21937730 21937730]; doi: [https://dx.doi.org/10.1074/mcp.M111.011429 10.1074/mcp.M111.011429]; GPMDB: [http://gpmdb.org/data/keyword/21937730 526].
+#Boisvert FM, Ahmad Y, Gierliński M, Charrière F, Lamont D, Scott M, Barton G, Lamond AI,  (2012) &quot;A quantitative spatial proteomics analysis of proteome turnover in human cells.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):M111.011429; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21937730 21937730]; doi: [https://dx.doi.org/10.1074/mcp.M111.011429 10.1074/mcp.M111.011429]; GPMDB: [http://gpmdb.org/data/keyword/21937730 526].
-#Nishtala K, Phong TQ, Steil L, Sauter M, Salazar MG, Kandolf R, Kroemer HK, Felix SB, VÃ¶lker U, Klingel K, Hammer E,  (2011) &quot;Virus-induced dilated cardiomyopathy is characterized by increased levels of fibrotic extracellular matrix proteins and reduced amounts of energy-producing enzymes.&quot; <i>Proteomics</i> <b>11</b>(22):4310&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21954127 21954127]; doi: [https://dx.doi.org/10.1002/pmic.201100229 10.1002/pmic.201100229]; GPMDB: [http://gpmdb.org/data/keyword/21954127 91].
+#Nishtala K, Phong TQ, Steil L, Sauter M, Salazar MG, Kandolf R, Kroemer HK, Felix SB, Völker U, Klingel K, Hammer E,  (2011) &quot;Virus-induced dilated cardiomyopathy is characterized by increased levels of fibrotic extracellular matrix proteins and reduced amounts of energy-producing enzymes.&quot; <i>Proteomics</i> <b>11</b>(22):4310&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21954127 21954127]; doi: [https://dx.doi.org/10.1002/pmic.201100229 10.1002/pmic.201100229]; GPMDB: [http://gpmdb.org/data/keyword/21954127 91].
 #Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M,  (2012) &quot;A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):O111.009613; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21964433 21964433]; doi: [https://dx.doi.org/10.1074/mcp.O111.009613 10.1074/mcp.O111.009613]; GPMDB: [http://gpmdb.org/data/keyword/21964433 138].
 # () &quot;&quot; <i></i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/ ]; GPMDB: [http://gpmdb.org/data/keyword/21969610 52].
@@ Line 304: / Line 304: @@
 #Capuano F, Bond NJ, Gatto L, Beaudoin F, Napier JA, Benvenuto E, Lilley KS, Baschieri S,  (2011) &quot;LC-MS/MS methods for absolute quantification and identification of proteins associated with chimeric plant oil bodies.&quot; <i>Anal Chem</i> <b>83</b>(24):9267&ndash;72; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22017570 22017570]; doi: [https://dx.doi.org/10.1021/ac201733m 10.1021/ac201733m]; GPMDB: [http://gpmdb.org/data/keyword/22017570 3].
 #Nagaraj N, Kulak NA, Cox J, Neuhauser N, Mayr K, Hoerning O, Vorm O, Mann M,  (2012) &quot;System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):M111.013722; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22021278 22021278]; doi: [https://dx.doi.org/10.1074/mcp.M111.013722 10.1074/mcp.M111.013722]; GPMDB: [http://gpmdb.org/data/keyword/22021278 13].
-#Bedon F, Villar E, Vincent D, Dupuy JW, Lomenech AM, Mabialangoma A, Chaumeil P, BarrÃ© A, Plomion C, Gion JM,  (2012) &quot;Proteomic plasticity of two Eucalyptus genotypes under contrasted water regimes in the field.&quot; <i>Plant Cell Environ</i> <b>35</b>(4):790&ndash;805; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22026815 22026815]; doi: [https://dx.doi.org/10.1111/j.1365-3040.2011.02452.x 10.1111/j.1365-3040.2011.02452.x]; GPMDB: [http://gpmdb.org/data/keyword/22026815 145].
+#Bedon F, Villar E, Vincent D, Dupuy JW, Lomenech AM, Mabialangoma A, Chaumeil P, Barré A, Plomion C, Gion JM,  (2012) &quot;Proteomic plasticity of two Eucalyptus genotypes under contrasted water regimes in the field.&quot; <i>Plant Cell Environ</i> <b>35</b>(4):790&ndash;805; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22026815 22026815]; doi: [https://dx.doi.org/10.1111/j.1365-3040.2011.02452.x 10.1111/j.1365-3040.2011.02452.x]; GPMDB: [http://gpmdb.org/data/keyword/22026815 145].
 #Inder KL, Zheng YZ, Davis MJ, Moon H, Loo D, Nguyen H, Clements JA, Parton RG, Foster LJ, Hill MM,  (2012) &quot;Expression of PTRF in PC-3 Cells modulates cholesterol dynamics and the actin cytoskeleton impacting secretion pathways.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(2):M111.012245; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22030351 22030351]; doi: [https://dx.doi.org/10.1074/mcp.M111.012245 10.1074/mcp.M111.012245]; GPMDB: [http://gpmdb.org/data/keyword/22030351 16].
 #Dunne JC, Li D, Kelly WJ, Leahy SC, Bond JJ, Attwood GT, Jordan TW,  (2012) &quot;Extracellular polysaccharide-degrading proteome of Butyrivibrio proteoclasticus.&quot; <i>J Proteome Res</i> <b>11</b>(1):131&ndash;42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22060546 22060546]; doi: [https://dx.doi.org/10.1021/pr200864j 10.1021/pr200864j]; GPMDB: [http://gpmdb.org/data/keyword/22060546 2].
-#Winck FV, RiaÃ±o-PachÃ³n DM, Sommer F, Rupprecht J, Mueller-Roeber B,  (2012) &quot;The nuclear proteome of the green alga Chlamydomonas reinhardtii.&quot; <i>Proteomics</i> <b>12</b>(1):95&ndash;100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22065562 22065562]; doi: [https://dx.doi.org/10.1002/pmic.201000782 10.1002/pmic.201000782]; GPMDB: [http://gpmdb.org/data/keyword/22065562 1].
+#Winck FV, Riaño-Pachón DM, Sommer F, Rupprecht J, Mueller-Roeber B,  (2012) &quot;The nuclear proteome of the green alga Chlamydomonas reinhardtii.&quot; <i>Proteomics</i> <b>12</b>(1):95&ndash;100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22065562 22065562]; doi: [https://dx.doi.org/10.1002/pmic.201000782 10.1002/pmic.201000782]; GPMDB: [http://gpmdb.org/data/keyword/22065562 1].
-#Hegemann B, Hutchins JR, Hudecz O, Novatchkova M, Rameseder J, Sykora MM, Liu S, Mazanek M, LÃ©nÃ¡rt P, HÃ©richÃ© JK, Poser I, Kraut N, Hyman AA, Yaffe MB, Mechtler K, Peters JM,  (2011) &quot;Systematic phosphorylation analysis of human mitotic protein complexes.&quot; <i>Sci Signal</i> <b>4</b>(198):rs12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22067460 22067460]; doi: [https://dx.doi.org/10.1126/scisignal.2001993 10.1126/scisignal.2001993]; GPMDB: [http://gpmdb.org/data/keyword/22067460 213].
+#Hegemann B, Hutchins JR, Hudecz O, Novatchkova M, Rameseder J, Sykora MM, Liu S, Mazanek M, Lénárt P, Hériché JK, Poser I, Kraut N, Hyman AA, Yaffe MB, Mechtler K, Peters JM,  (2011) &quot;Systematic phosphorylation analysis of human mitotic protein complexes.&quot; <i>Sci Signal</i> <b>4</b>(198):rs12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22067460 22067460]; doi: [https://dx.doi.org/10.1126/scisignal.2001993 10.1126/scisignal.2001993]; GPMDB: [http://gpmdb.org/data/keyword/22067460 213].
-#Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, JÃ¼nger MA, KÃ¶hler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M,  (2011) &quot;Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome.&quot; <i>Mol Syst Biol</i> <b>7</b>:547; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22068330 22068330]; doi: [https://dx.doi.org/10.1038/msb.2011.79 10.1038/msb.2011.79]; GPMDB: [http://gpmdb.org/data/keyword/22068330 138].
+#Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M,  (2011) &quot;Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome.&quot; <i>Mol Syst Biol</i> <b>7</b>:547; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22068330 22068330]; doi: [https://dx.doi.org/10.1038/msb.2011.79 10.1038/msb.2011.79]; GPMDB: [http://gpmdb.org/data/keyword/22068330 138].
-#Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, PÃ¤Ã¤bo S, Mann M,  (2011) &quot;Deep proteome and transcriptome mapping of a human cancer cell line.&quot; <i>Mol Syst Biol</i> <b>7</b>:548; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22068331 22068331]; doi: [https://dx.doi.org/10.1038/msb.2011.81 10.1038/msb.2011.81]; GPMDB: [http://gpmdb.org/data/keyword/22068331 164].
+#Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Pääbo S, Mann M,  (2011) &quot;Deep proteome and transcriptome mapping of a human cancer cell line.&quot; <i>Mol Syst Biol</i> <b>7</b>:548; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22068331 22068331]; doi: [https://dx.doi.org/10.1038/msb.2011.81 10.1038/msb.2011.81]; GPMDB: [http://gpmdb.org/data/keyword/22068331 164].
 #Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R,  (2011) &quot;The quantitative proteome of a human cell line.&quot; <i>Mol Syst Biol</i> <b>7</b>:549; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22068332 22068332]; doi: [https://dx.doi.org/10.1038/msb.2011.82 10.1038/msb.2011.82]; GPMDB: [http://gpmdb.org/data/keyword/22068332 60].
 #Okamoto A, Yamada K,  (2011) &quot;Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome.&quot; <i>BMC Microbiol</i> <b>11</b>:249; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22070424 22070424]; doi: [https://dx.doi.org/10.1186/1471-2180-11-249 10.1186/1471-2180-11-249]; GPMDB: [http://gpmdb.org/data/keyword/22070424 2].
@@ Line 320: / Line 320: @@
 #Barbhuiya MA, Sahasrabuddhe NA, Pinto SM, Muthusamy B, Singh TD, Nanjappa V, Keerthikumar S, Delanghe B, Harsha HC, Chaerkady R, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, Pandey A,  (2011) &quot;Comprehensive proteomic analysis of human bile.&quot; <i>Proteomics</i> <b>11</b>(23):4443&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22114102 22114102]; doi: [https://dx.doi.org/10.1002/pmic.201100197 10.1002/pmic.201100197]; GPMDB: [http://gpmdb.org/data/keyword/22114102 37].
 #Wright B, Stanley RG, Kaiser WJ, Mills DJ, Gibbins JM,  (2011) &quot;Analysis of protein networks in resting and collagen receptor (GPVI)-stimulated platelet sub-proteomes.&quot; <i>Proteomics</i> <b>11</b>(23):4588&ndash;92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22114104 22114104]; doi: [https://dx.doi.org/10.1002/pmic.201100410 10.1002/pmic.201100410]; GPMDB: [http://gpmdb.org/data/keyword/22114104 24].
-#MalmstrÃ¶m J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, MalmstrÃ¶m L, BjÃ¶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].
+#Malmström J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmström L, Björck 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].
 #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].
-#Journet A, Klein G, BrugiÃ¨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].
+#Journet A, Klein G, Brugière 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].
 #Murray CI, Uhrigshardt H, O'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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 #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].
-#Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, STREAM Consortium, Wohlleben W, RodrÃguez-GarcÃa A, MartÃn 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].
+#Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, STREAM Consortium, Wohlleben W, Rodríguez-García A, Martín 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].
 #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].
 #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].
-#Michalski A, Damoc E, Lange O, Denisov E, Nolting D, MÃ¼ller 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].
+#Michalski A, Damoc E, Lange O, Denisov E, Nolting D, Müller 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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@@ Line 340: / Line 340: @@
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-#KÃ¶nig S, Nimtz M, Scheiter M, Ljunggren HG, Bryceson YT, JÃ¤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].
+#König S, Nimtz M, Scheiter M, Ljunggren HG, Bryceson YT, Jänsch 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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-#Capriotti AL, Caracciolo G, Caruso G, Cavaliere C, Pozzi D, Samperi R, LaganÃ  A,  (2013) &quot;Label-free quantitative analysis for studying the interactions between nanoparticles and plasma proteins.&quot; <i>Anal Bioanal Chem</i> <b>405</b>(2-3):635&ndash;45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22274284 22274284]; doi: [https://dx.doi.org/10.1007/s00216-011-5691-y 10.1007/s00216-011-5691-y]; GPMDB: [http://gpmdb.org/data/keyword/22274284 45].
+#Capriotti AL, Caracciolo G, Caruso G, Cavaliere C, Pozzi D, Samperi R, Laganà A,  (2013) &quot;Label-free quantitative analysis for studying the interactions between nanoparticles and plasma proteins.&quot; <i>Anal Bioanal Chem</i> <b>405</b>(2-3):635&ndash;45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22274284 22274284]; doi: [https://dx.doi.org/10.1007/s00216-011-5691-y 10.1007/s00216-011-5691-y]; GPMDB: [http://gpmdb.org/data/keyword/22274284 45].
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@@ Line 358: / Line 358: @@
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-#Tondeleir D, Lambrechts A, MÃ¼ller 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 Î²-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].
+#Tondeleir D, Lambrechts A, Müller 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 β-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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-#Wright JC, Collins MO, Yu L, KÃ¤ll L, Brosch M, Choudhary JS,  (2012) &quot;Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(8):478&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22493177 22493177]; doi: [https://dx.doi.org/10.1074/mcp.O111.014522 10.1074/mcp.O111.014522]; GPMDB: [http://gpmdb.org/data/keyword/22493177 8].
+#Wright JC, Collins MO, Yu L, Käll L, Brosch M, Choudhary JS,  (2012) &quot;Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(8):478&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22493177 22493177]; doi: [https://dx.doi.org/10.1074/mcp.O111.014522 10.1074/mcp.O111.014522]; GPMDB: [http://gpmdb.org/data/keyword/22493177 8].
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@@ Line 368: / Line 368: @@
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-#Byron A, Humphries JD, Craig SE, Knight D, Humphries MJ,  (2012) &quot;Proteomic analysis of Î±4Î²1 integrin adhesion complexes reveals Î±-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].
+#Byron A, Humphries JD, Craig SE, Knight D, Humphries MJ,  (2012) &quot;Proteomic analysis of α4β1 integrin adhesion complexes reveals α-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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-#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, AnÃ© 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].
+#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, Ané 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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+#Vialás V, Perumal P, Gutierrez D, Ximénez-Embún P, Nombela C, Gil C, Chaffin WL,  (2012) &quot;Cell surface shaving of Candida albicans biofilms, hyphae, and yeast form cells.&quot; <i>Proteomics</i> <b>12</b>(14):2331&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22685022 22685022]; doi: [https://dx.doi.org/10.1002/pmic.201100588 10.1002/pmic.201100588]; GPMDB: [http://gpmdb.org/data/keyword/22685022 1].
-#MuÃ±oz J, Stange DE, Schepers AG, van de Wetering M, Koo BK, Itzkovitz S, Volckmann R, Kung KS, Koster J, Radulescu S, Myant K, Versteeg R, Sansom OJ, van Es JH, Barker N, van Oudenaarden A, Mohammed S, Heck AJ, Clevers H,  (2012) &quot;The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers.&quot; <i>EMBO J</i> <b>31</b>(14):3079&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22692129 22692129]; doi: [https://dx.doi.org/10.1038/emboj.2012.166 10.1038/emboj.2012.166]; GPMDB: [http://gpmdb.org/data/keyword/22692129 106].
+#Muñoz J, Stange DE, Schepers AG, van de Wetering M, Koo BK, Itzkovitz S, Volckmann R, Kung KS, Koster J, Radulescu S, Myant K, Versteeg R, Sansom OJ, van Es JH, Barker N, van Oudenaarden A, Mohammed S, Heck AJ, Clevers H,  (2012) &quot;The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers.&quot; <i>EMBO J</i> <b>31</b>(14):3079&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22692129 22692129]; doi: [https://dx.doi.org/10.1038/emboj.2012.166 10.1038/emboj.2012.166]; GPMDB: [http://gpmdb.org/data/keyword/22692129 106].
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@@ Line 390: / Line 390: @@
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+#Corthals A, Koller A, Martin DW, Rieger R, Chen EI, Bernaski M, Recagno G, Dávalos LM,  (2012) &quot;Detecting the immune system response of a 500 year-old Inca mummy.&quot; <i>PLoS One</i> <b>7</b>(7):e41244; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22848450 22848450]; doi: [https://dx.doi.org/10.1371/journal.pone.0041244 10.1371/journal.pone.0041244]; GPMDB: [http://gpmdb.org/data/keyword/22848450 12].
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@@ Line 403: / Line 403: @@
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+#Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W,  (2012) &quot;Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit.&quot; <i>Mol Syst Biol</i> <b>8</b>:606; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22929616 22929616]; doi: [https://dx.doi.org/10.1038/msb.2012.39 10.1038/msb.2012.39]; GPMDB: [http://gpmdb.org/data/keyword/22929616 24].
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@@ Line 412: / Line 412: @@
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+#Motohashi R, Rödiger A, Agne B, Baerenfaller K, Baginsky S,  (2012) &quot;Common and specific protein accumulation patterns in different albino/pale-green mutants reveals regulon organization at the proteome level.&quot; <i>Plant Physiol</i> <b>160</b>(4):2189&ndash;201; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23027667 23027667]; doi: [https://dx.doi.org/10.1104/pp.112.204032 10.1104/pp.112.204032]; GPMDB: [http://gpmdb.org/data/keyword/23027667 4].
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+#Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA,  (2013) &quot;Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(3):825&ndash;31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23266961 23266961]; doi: [https://dx.doi.org/10.1074/mcp.O112.027094 10.1074/mcp.O112.027094]; GPMDB: [http://gpmdb.org/data/keyword/23266961 72].
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@@ Line 442: / Line 442: @@
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+#Albrethsen J, Agner J, Piersma SR, Højrup P, Pham TV, Weldingh K, Jimenez CR, Andersen P, Rosenkrands I,  (2013) &quot;Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(5):1180&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23345537 23345537]; doi: [https://dx.doi.org/10.1074/mcp.M112.018846 10.1074/mcp.M112.018846]; GPMDB: [http://gpmdb.org/data/keyword/23345537 59].
-#HauÃŸmann U, Wolters DA, FrÃ¤nzel B, Eltis LD, Poetsch A,  (2013) &quot;Physiological adaptation of the Rhodococcus jostii RHA1 membrane proteome to steroids as growth substrates.&quot; <i>J Proteome Res</i> <b>12</b>(3):1188&ndash;98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23360181 23360181]; doi: [https://dx.doi.org/10.1021/pr300816n 10.1021/pr300816n]; GPMDB: [http://gpmdb.org/data/keyword/23360181 220].
+#Haußmann U, Wolters DA, Fränzel B, Eltis LD, Poetsch A,  (2013) &quot;Physiological adaptation of the Rhodococcus jostii RHA1 membrane proteome to steroids as growth substrates.&quot; <i>J Proteome Res</i> <b>12</b>(3):1188&ndash;98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23360181 23360181]; doi: [https://dx.doi.org/10.1021/pr300816n 10.1021/pr300816n]; GPMDB: [http://gpmdb.org/data/keyword/23360181 220].
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-#Zanivan S, Meves A, Behrendt K, Schoof EM, Neilson LJ, Cox J, Tang HR, Kalna G, van Ree JH, van Deursen JM, Trempus CS, Machesky LM, Linding R, WickstrÃ¶m SA, FÃ¤ssler R, Mann M,  (2013) &quot;In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis.&quot; <i>Cell Rep</i> <b>3</b>(2):552&ndash;66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23375375 23375375]; doi: [https://dx.doi.org/10.1016/j.celrep.2013.01.003 10.1016/j.celrep.2013.01.003]; GPMDB: [http://gpmdb.org/data/keyword/23375375 315].
+#Zanivan S, Meves A, Behrendt K, Schoof EM, Neilson LJ, Cox J, Tang HR, Kalna G, van Ree JH, van Deursen JM, Trempus CS, Machesky LM, Linding R, Wickström SA, Fässler R, Mann M,  (2013) &quot;In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis.&quot; <i>Cell Rep</i> <b>3</b>(2):552&ndash;66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23375375 23375375]; doi: [https://dx.doi.org/10.1016/j.celrep.2013.01.003 10.1016/j.celrep.2013.01.003]; GPMDB: [http://gpmdb.org/data/keyword/23375375 315].
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+#Cho CK, Drabovich AP, Karagiannis GS, Martínez-Morillo E, Dason S, Dimitromanolakis A, Diamandis EP,  (2013) &quot;Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome.&quot; <i>Clin Proteomics</i> <b>10</b>(1):2; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23394617 23394617]; doi: [https://dx.doi.org/10.1186/1559-0275-10-2 10.1186/1559-0275-10-2]; GPMDB: [http://gpmdb.org/data/keyword/23394617 30].
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-#Colinet H, Overgaard J, Com E, SÃ¸rensen JG,  (2013) &quot;Proteomic profiling of thermal acclimation in Drosophila melanogaster.&quot; <i>Insect Biochem Mol Biol</i> <b>43</b>(4):352&ndash;65; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23416132 23416132]; doi: [https://dx.doi.org/10.1016/j.ibmb.2013.01.006 10.1016/j.ibmb.2013.01.006]; GPMDB: [http://gpmdb.org/data/keyword/23416132 50].
+#Colinet H, Overgaard J, Com E, Sørensen JG,  (2013) &quot;Proteomic profiling of thermal acclimation in Drosophila melanogaster.&quot; <i>Insect Biochem Mol Biol</i> <b>43</b>(4):352&ndash;65; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23416132 23416132]; doi: [https://dx.doi.org/10.1016/j.ibmb.2013.01.006 10.1016/j.ibmb.2013.01.006]; GPMDB: [http://gpmdb.org/data/keyword/23416132 50].
-#Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, MÃ¼nzel M, Wagner M, MÃ¼ller M, Khan F, Eberl HC, Mensinga A, Brinkman AB, Lephikov K, MÃ¼ller U, Walter J, Boelens R, van Ingen H, Leonhardt H, Carell T, Vermeulen M,  (2013) &quot;Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives.&quot; <i>Cell</i> <b>152</b>(5):1146&ndash;59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23434322 23434322]; doi: [https://dx.doi.org/10.1016/j.cell.2013.02.004 10.1016/j.cell.2013.02.004]; GPMDB: [http://gpmdb.org/data/keyword/23434322 249].
+#Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, Münzel M, Wagner M, Müller M, Khan F, Eberl HC, Mensinga A, Brinkman AB, Lephikov K, Müller U, Walter J, Boelens R, van Ingen H, Leonhardt H, Carell T, Vermeulen M,  (2013) &quot;Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives.&quot; <i>Cell</i> <b>152</b>(5):1146&ndash;59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23434322 23434322]; doi: [https://dx.doi.org/10.1016/j.cell.2013.02.004 10.1016/j.cell.2013.02.004]; GPMDB: [http://gpmdb.org/data/keyword/23434322 249].
-#Chapel A, Kieffer-Jaquinod S, SagnÃ© C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A,  (2013) &quot;An extended proteome map of the lysosomal membrane reveals novel potential transporters.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(6):1572&ndash;88; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23436907 23436907]; doi: [https://dx.doi.org/10.1074/mcp.M112.021980 10.1074/mcp.M112.021980]; GPMDB: [http://gpmdb.org/data/keyword/23436907 1].
+#Chapel A, Kieffer-Jaquinod S, Sagné C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A,  (2013) &quot;An extended proteome map of the lysosomal membrane reveals novel potential transporters.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(6):1572&ndash;88; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23436907 23436907]; doi: [https://dx.doi.org/10.1074/mcp.M112.021980 10.1074/mcp.M112.021980]; GPMDB: [http://gpmdb.org/data/keyword/23436907 1].
-#Fabietti A, Gaspari M, Krishnan S, Quirino A, Liberto MC, Cuda G, FocÃ  A,  (2013) &quot;Shotgun proteomic analysis of two Bartonella quintana strains.&quot; <i>Proteomics</i> <b>13</b>(8):1375&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23450663 23450663]; doi: [https://dx.doi.org/10.1002/pmic.201200165 10.1002/pmic.201200165]; GPMDB: [http://gpmdb.org/data/keyword/23450663 8].
+#Fabietti A, Gaspari M, Krishnan S, Quirino A, Liberto MC, Cuda G, Focà A,  (2013) &quot;Shotgun proteomic analysis of two Bartonella quintana strains.&quot; <i>Proteomics</i> <b>13</b>(8):1375&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23450663 23450663]; doi: [https://dx.doi.org/10.1002/pmic.201200165 10.1002/pmic.201200165]; GPMDB: [http://gpmdb.org/data/keyword/23450663 8].
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-#Gunaratne J, Schmidt A, Quandt A, Neo SP, SaraÃ§ OS, Gracia T, Loguercio S, AhrnÃ© E, Xia RL, Tan KH, LÃ¶ssner C, BÃ¤hler J, Beyer A, Blackstock W, Aebersold R,  (2013) &quot;Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(6):1741&ndash;51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23462206 23462206]; doi: [https://dx.doi.org/10.1074/mcp.M112.023754 10.1074/mcp.M112.023754]; GPMDB: [http://gpmdb.org/data/keyword/23462206 384].
+#Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R,  (2013) &quot;Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(6):1741&ndash;51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23462206 23462206]; doi: [https://dx.doi.org/10.1074/mcp.M112.023754 10.1074/mcp.M112.023754]; GPMDB: [http://gpmdb.org/data/keyword/23462206 384].
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 #Urbaniak MD, Martin DM, Ferguson MA,  (2013) &quot;Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei.&quot; <i>J Proteome Res</i> <b>12</b>(5):2233&ndash;44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23485197 23485197]; doi: [https://dx.doi.org/10.1021/pr400086y 10.1021/pr400086y]; GPMDB: [http://gpmdb.org/data/keyword/23485197 148].
 #van Nuland R, Smits AH, Pallaki P, Jansen PW, Vermeulen M, Timmers HT,  (2013) &quot;Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes.&quot; <i>Mol Cell Biol</i> <b>33</b>(10):2067&ndash;77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23508102 23508102]; doi: [https://dx.doi.org/10.1128/MCB.01742-12 10.1128/MCB.01742-12]; GPMDB: [http://gpmdb.org/data/keyword/23508102 52].
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-#Ori A, Banterle N, Iskar M, AndrÃ©s-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M,  (2013) &quot;Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.&quot; <i>Mol Syst Biol</i> <b>9</b>:648; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23511206 23511206]; doi: [https://dx.doi.org/10.1038/msb.2013.4 10.1038/msb.2013.4]; GPMDB: [http://gpmdb.org/data/keyword/23511206 30].
+#Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M,  (2013) &quot;Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.&quot; <i>Mol Syst Biol</i> <b>9</b>:648; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23511206 23511206]; doi: [https://dx.doi.org/10.1038/msb.2013.4 10.1038/msb.2013.4]; GPMDB: [http://gpmdb.org/data/keyword/23511206 30].
-#Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, KÃ¤ll L, Elofsson A,  (2013) &quot;Membrane protein shaving with thermolysin can be used to evaluate topology predictors.&quot; <i>Proteomics</i> <b>13</b>(9):1467&ndash;80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23512833 23512833]; doi: [https://dx.doi.org/10.1002/pmic.201200517 10.1002/pmic.201200517]; GPMDB: [http://gpmdb.org/data/keyword/23512833 8].
+#Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A,  (2013) &quot;Membrane protein shaving with thermolysin can be used to evaluate topology predictors.&quot; <i>Proteomics</i> <b>13</b>(9):1467&ndash;80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23512833 23512833]; doi: [https://dx.doi.org/10.1002/pmic.201200517 10.1002/pmic.201200517]; GPMDB: [http://gpmdb.org/data/keyword/23512833 8].
 #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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@@ Line 477: / Line 477: @@
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+#Bottermann K, Reinartz M, Barsoum M, Kötter S, Gödecke A,  (2013) &quot;Systematic Analysis Reveals Elongation Factor 2 and α-Enolase as Novel Interaction Partners of AKT2.&quot; <i>PLoS One</i> <b>8</b>(6):e66045; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23823123 23823123]; doi: [https://dx.doi.org/10.1371/journal.pone.0066045 10.1371/journal.pone.0066045]; GPMDB: [http://gpmdb.org/data/keyword/23823123 4].
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+#Xia L, Wang TD, Shen SM, Zhao M, Sun H, He Y, Xie L, Wu ZX, Han SF, Wang LS, Chen GQ,  (2013) &quot;Phosphoproteomics study on the activated PKCδ-induced cell death.&quot; <i>J Proteome Res</i> <b>12</b>(10):4280&ndash;301; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23879269 23879269]; doi: [https://dx.doi.org/10.1021/pr400089v 10.1021/pr400089v]; GPMDB: [http://gpmdb.org/data/keyword/23879269 385].
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+#Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL,  (2013) &quot;A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies.&quot; <i>J Proteome Res</i> <b>12</b>(9):4005&ndash;17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23901793 23901793]; doi: [https://dx.doi.org/10.1021/pr400309p 10.1021/pr400309p]; GPMDB: [http://gpmdb.org/data/keyword/23901793 56].
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@@ Line 525: / Line 525: @@
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+#Liu NQ, Dekker LJ, Stingl C, Güzel C, De Marchi T, Martens JW, Foekens JA, Luider TM, Umar A,  (2013) &quot;Quantitative proteomic analysis of microdissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches.&quot; <i>J Proteome Res</i> <b>12</b>(10):4627&ndash;41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23957277 23957277]; doi: [https://dx.doi.org/10.1021/pr4005794 10.1021/pr4005794]; GPMDB: [http://gpmdb.org/data/keyword/23957277 57].
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+#Hahne H, Pachl F, Ruprecht B, Maier SK, Klaeger S, Helm D, Médard G, Wilm M, Lemeer S, Kuster B,  (2013) &quot;DMSO enhances electrospray response, boosting sensitivity of proteomic experiments.&quot; <i>Nat Methods</i> <b>10</b>(10):989&ndash;91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23975139 23975139]; doi: [https://dx.doi.org/10.1038/nmeth.2610 10.1038/nmeth.2610]; GPMDB: [http://gpmdb.org/data/keyword/23975139 64].
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+#Zanivan S, Maione F, Hein MY, Hernández-Fernaud JR, Ostasiewicz P, Giraudo E, Mann M,  (2013) &quot;SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers.&quot; <i>Mol Cell Proteomics</i> <b>12</b>(12):3599&ndash;611; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23979707 23979707]; doi: [https://dx.doi.org/10.1074/mcp.M113.031344 10.1074/mcp.M113.031344]; GPMDB: [http://gpmdb.org/data/keyword/23979707 452].
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@@ Line 534: / Line 534: @@
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+#Carlson SM, Moore KE, Green EM, Martín GM, Gozani O,  (2014) &quot;Proteome-wide enrichment of proteins modified by lysine methylation.&quot; <i>Nat Protoc</i> <b>9</b>(1):37&ndash;50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24309976 24309976]; doi: [https://dx.doi.org/10.1038/nprot.2013.164 10.1038/nprot.2013.164]; GPMDB: [http://gpmdb.org/data/keyword/24309976 8].
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@@ Line 581: / Line 581: @@
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+#Lange PF, Huesgen PF, Nguyen K, Overall CM,  (2014) &quot;Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome.&quot; <i>J Proteome Res</i> <b>13</b>(4):2028&ndash;44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24555563 24555563]; doi: [https://dx.doi.org/10.1021/pr401191w 10.1021/pr401191w]; GPMDB: [http://gpmdb.org/data/keyword/24555563 101].
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+#Plohnke N, Hamann A, Poetsch A, Osiewacz HD, Rögner M, Rexroth S,  (2014) &quot;Proteomic analysis of mitochondria from senescent Podospora anserina casts new light on ROS dependent aging mechanisms.&quot; <i>Exp Gerontol</i> <b>56</b>:13&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24556281 24556281]; doi: [https://dx.doi.org/10.1016/j.exger.2014.02.008 10.1016/j.exger.2014.02.008]; GPMDB: [http://gpmdb.org/data/keyword/24556281 36].
-#Kolinko I, LohÃŸe A, Borg S, Raschdorf O, Jogler C, Tu Q, PÃ³sfai M, Tompa E, Plitzko JM, Brachmann A, Wanner G, MÃ¼ller R, Zhang Y, SchÃ¼ler D,  (2014) &quot;Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters.&quot; <i>Nat Nanotechnol</i> <b>9</b>(3):193&ndash;7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24561353 24561353]; doi: [https://dx.doi.org/10.1038/nnano.2014.13 10.1038/nnano.2014.13]; GPMDB: [http://gpmdb.org/data/keyword/24561353 1].
+#Kolinko I, Lohße A, Borg S, Raschdorf O, Jogler C, Tu Q, Pósfai M, Tompa E, Plitzko JM, Brachmann A, Wanner G, Müller R, Zhang Y, Schüler D,  (2014) &quot;Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters.&quot; <i>Nat Nanotechnol</i> <b>9</b>(3):193&ndash;7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24561353 24561353]; doi: [https://dx.doi.org/10.1038/nnano.2014.13 10.1038/nnano.2014.13]; GPMDB: [http://gpmdb.org/data/keyword/24561353 1].
 #Sigdel TK, Nicora CD, Hsieh SC, Dai H, Qian WJ, Camp DG 2nd, Sarwal MM,  (2014) &quot;Optimization for peptide sample preparation for urine peptidomics.&quot; <i>Clin Proteomics</i> <b>11</b>(1):7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24568099 24568099]; doi: [https://dx.doi.org/10.1186/1559-0275-11-7 10.1186/1559-0275-11-7]; GPMDB: [http://gpmdb.org/data/keyword/24568099 8].
 #Husi H, Van Agtmael T, Mullen W, Bahlmann FH, Schanstra JP, Vlahou A, Delles C, Perco P, Mischak H,  (2014) &quot;Proteome-based systems biology analysis of the diabetic mouse aorta reveals major changes in fatty acid biosynthesis as potential hallmark in diabetes mellitus-associated vascular disease.&quot; <i>Circ Cardiovasc Genet</i> <b>7</b>(2):161&ndash;70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24573165 24573165]; doi: [https://dx.doi.org/10.1161/CIRCGENETICS.113.000196 10.1161/CIRCGENETICS.113.000196]; GPMDB: [http://gpmdb.org/data/keyword/24573165 14].
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 #Benevento M, Di Palma S, Snijder J, Moyer CL, Reddy VS, Nemerow GR, Heck AJ,  (2014) &quot;Adenovirus composition, proteolysis, and disassembly studied by in-depth qualitative and quantitative proteomics.&quot; <i>J Biol Chem</i> <b>289</b>(16):11421&ndash;30; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24591515 24591515]; doi: [https://dx.doi.org/10.1074/jbc.M113.537498 10.1074/jbc.M113.537498]; GPMDB: [http://gpmdb.org/data/keyword/24591515 5].
-#Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, CoutÃ© Y, Rivkina E, Abergel C, Claverie JM,  (2014) &quot;Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.&quot; <i>Proc Natl Acad Sci U S A</i> <b>111</b>(11):4274&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24591590 24591590]; doi: [https://dx.doi.org/10.1073/pnas.1320670111 10.1073/pnas.1320670111]; GPMDB: [http://gpmdb.org/data/keyword/24591590 1].
+#Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM,  (2014) &quot;Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.&quot; <i>Proc Natl Acad Sci U S A</i> <b>111</b>(11):4274&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24591590 24591590]; doi: [https://dx.doi.org/10.1073/pnas.1320670111 10.1073/pnas.1320670111]; GPMDB: [http://gpmdb.org/data/keyword/24591590 1].
 #Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR, Lamond AI,  (2014) &quot;A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells.&quot; <i>Elife</i> <b>3</b>:e01630; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24596151 24596151]; GPMDB: [http://gpmdb.org/data/keyword/24596151 98].
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@@ Line 616: / Line 616: @@
 #Peebo K, Valgepea K, Nahku R, Riis G, Oun M, Adamberg K, Vilu R,  (2014) &quot;Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli.&quot; <i>Appl Microbiol Biotechnol</i> <b>98</b>(11):5131&ndash;43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24633370 24633370]; doi: [https://dx.doi.org/10.1007/s00253-014-5613-y 10.1007/s00253-014-5613-y]; GPMDB: [http://gpmdb.org/data/keyword/24633370 10].
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-#de Groot RE, Ganji RS, Bernatik O, Lloyd-Lewis B, Seipel K, Å edovÃ¡ K, ZdrÃ¡hal Z, Dhople VM, Dale TC, Korswagen HC, Bryja V,  (2014) &quot;Huwe1-mediated ubiquitylation of dishevelled defines a negative feedback loop in the Wnt signaling pathway.&quot; <i>Sci Signal</i> <b>7</b>(317):ra26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24643799 24643799]; doi: [https://dx.doi.org/10.1126/scisignal.2004985 10.1126/scisignal.2004985]; GPMDB: [http://gpmdb.org/data/keyword/24643799 10].
+#de Groot RE, Ganji RS, Bernatik O, Lloyd-Lewis B, Seipel K, Šedová K, Zdráhal Z, Dhople VM, Dale TC, Korswagen HC, Bryja V,  (2014) &quot;Huwe1-mediated ubiquitylation of dishevelled defines a negative feedback loop in the Wnt signaling pathway.&quot; <i>Sci Signal</i> <b>7</b>(317):ra26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24643799 24643799]; doi: [https://dx.doi.org/10.1126/scisignal.2004985 10.1126/scisignal.2004985]; GPMDB: [http://gpmdb.org/data/keyword/24643799 10].
 #Sahasrabuddhe NA, Barbhuiya MA, Bhunia S, Subbannayya T, Gowda H, Advani J, Shrivastav BR, Navani S, Leal P, Roa JC, Chaerkady R, Gupta S, Chatterjee A, Pandey A, Tiwari PK,  (2014) &quot;Identification of prosaposin and transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics.&quot; <i>Biochem Biophys Res Commun</i> <b>446</b>(4):863&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24657443 24657443]; doi: [https://dx.doi.org/10.1016/j.bbrc.2014.03.017 10.1016/j.bbrc.2014.03.017]; GPMDB: [http://gpmdb.org/data/keyword/24657443 29].
 #Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LD, Balakrishnan L, Subbannayya T, Yan F, Prasad TS, Gowda H, Lee C, Hancock WS, Pandey A,  (2014) &quot;Functional annotation of proteome encoded by human chromosome 22.&quot; <i>J Proteome Res</i> <b>13</b>(6):2749&ndash;60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24669763 24669763]; doi: [https://dx.doi.org/10.1021/pr401169d 10.1021/pr401169d]; GPMDB: [http://gpmdb.org/data/keyword/24669763 88].
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-#Shevchuk O, Abidi N, Klawonn F, Wissing J, Nimtz M, Kugler C, Steinert M, Goldmann T, JÃ¤nsch L,  (2014) &quot;HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies.&quot; <i>J Proteome Res</i> <b>13</b>(11):5230&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24702127 24702127]; doi: [https://dx.doi.org/10.1021/pr500096a 10.1021/pr500096a]; GPMDB: [http://gpmdb.org/data/keyword/24702127 4].
+#Shevchuk O, Abidi N, Klawonn F, Wissing J, Nimtz M, Kugler C, Steinert M, Goldmann T, Jänsch L,  (2014) &quot;HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies.&quot; <i>J Proteome Res</i> <b>13</b>(11):5230&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24702127 24702127]; doi: [https://dx.doi.org/10.1021/pr500096a 10.1021/pr500096a]; GPMDB: [http://gpmdb.org/data/keyword/24702127 4].
+#Tsai CM, Wu HY, Su TH, Kuo CW, Huang HW, Chung CH, Chen CS, Khoo KH, Chen YJ, Lin KI,  (2014) &quot;Phosphoproteomic analyses reveal that galectin-1 augments the dynamics of B-cell receptor signaling.&quot; <i>J Proteomics</i> <b>103</b>:241&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24704852 24704852]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.03.031 10.1016/j.jprot.2014.03.031]; GPMDB: [http://gpmdb.org/data/keyword/24704852 15].
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-#Azimi A, Pernemalm M, Frostvik Stolt M, Hansson J, LehtiÃ¶ J, EgyhÃ¡zi Brage S, Hertzman Johansson C,  (2014) &quot;Proteomics analysis of melanoma metastases: association between S100A13 expression and chemotherapy resistance.&quot; <i>Br J Cancer</i> <b>110</b>(10):2489&ndash;95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24722184 24722184]; doi: [https://dx.doi.org/10.1038/bjc.2014.169 10.1038/bjc.2014.169]; GPMDB: [http://gpmdb.org/data/keyword/24722184 146].
+#Azimi A, Pernemalm M, Frostvik Stolt M, Hansson J, Lehtiö J, Egyházi Brage S, Hertzman Johansson C,  (2014) &quot;Proteomics analysis of melanoma metastases: association between S100A13 expression and chemotherapy resistance.&quot; <i>Br J Cancer</i> <b>110</b>(10):2489&ndash;95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24722184 24722184]; doi: [https://dx.doi.org/10.1038/bjc.2014.169 10.1038/bjc.2014.169]; GPMDB: [http://gpmdb.org/data/keyword/24722184 146].
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-#Farrelly LA, Dicker P, Wynne K, English J, Cagney G, FÃ¶cking M, Cotter DR,  (2014) &quot;Adolescent Risperidone treatment alters protein expression associated with protein trafficking and cellular metabolism in the adult rat prefrontal cortex.&quot; <i>Proteomics</i> <b>14</b>(12):1574&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24733778 24733778]; doi: [https://dx.doi.org/10.1002/pmic.201300466 10.1002/pmic.201300466]; GPMDB: [http://gpmdb.org/data/keyword/24733778 30].
+#Farrelly LA, Dicker P, Wynne K, English J, Cagney G, Föcking M, Cotter DR,  (2014) &quot;Adolescent Risperidone treatment alters protein expression associated with protein trafficking and cellular metabolism in the adult rat prefrontal cortex.&quot; <i>Proteomics</i> <b>14</b>(12):1574&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24733778 24733778]; doi: [https://dx.doi.org/10.1002/pmic.201300466 10.1002/pmic.201300466]; GPMDB: [http://gpmdb.org/data/keyword/24733778 30].
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-#Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, BÃ¶nisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A,  (2014) &quot;The histone variant H2A.Bbd is enriched at sites of DNA synthesis.&quot; <i>Nucleic Acids Res</i> <b>42</b>(10):6405&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24753410 24753410]; doi: [https://dx.doi.org/10.1093/nar/gku303 10.1093/nar/gku303]; GPMDB: [http://gpmdb.org/data/keyword/24753410 96].
+#Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, Bönisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A,  (2014) &quot;The histone variant H2A.Bbd is enriched at sites of DNA synthesis.&quot; <i>Nucleic Acids Res</i> <b>42</b>(10):6405&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24753410 24753410]; doi: [https://dx.doi.org/10.1093/nar/gku303 10.1093/nar/gku303]; GPMDB: [http://gpmdb.org/data/keyword/24753410 96].
 #Han D, Jin J, Woo J, Min H, Kim Y,  (2014) &quot;Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation.&quot; <i>Proteomics</i> <b>14</b>(13-14):1604&ndash;9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24753479 24753479]; doi: [https://dx.doi.org/10.1002/pmic.201300495 10.1002/pmic.201300495]; GPMDB: [http://gpmdb.org/data/keyword/24753479 107].
-#Chiasserini D, van Weering JR, Piersma SR, Pham TV, Malekzadeh A, Teunissen CE, de Wit H, JimÃ©nez CR,  (2014) &quot;Proteomic analysis of cerebrospinal fluid extracellular vesicles: a comprehensive dataset.&quot; <i>J Proteomics</i> <b>106</b>:191&ndash;204; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24769233 24769233]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.04.028 10.1016/j.jprot.2014.04.028]; GPMDB: [http://gpmdb.org/data/keyword/24769233 36].
+#Chiasserini D, van Weering JR, Piersma SR, Pham TV, Malekzadeh A, Teunissen CE, de Wit H, Jiménez CR,  (2014) &quot;Proteomic analysis of cerebrospinal fluid extracellular vesicles: a comprehensive dataset.&quot; <i>J Proteomics</i> <b>106</b>:191&ndash;204; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24769233 24769233]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.04.028 10.1016/j.jprot.2014.04.028]; GPMDB: [http://gpmdb.org/data/keyword/24769233 36].
 #Eravci M, Sommer C, Selbach M,  (2014) &quot;IPG strip-based peptide fractionation for shotgun proteomics.&quot; <i>Methods Mol Biol</i> <b>1156</b>:67&ndash;77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24791982 24791982]; doi: [https://dx.doi.org/10.1007/978-1-4939-0685-7_5 10.1007/978-1-4939-0685-7_5]; GPMDB: [http://gpmdb.org/data/keyword/24791982 41].
-#GÃ¼ther ML, Urbaniak MD, Tavendale A, Prescott A, Ferguson MA,  (2014) &quot;High-confidence glycosome proteome for procyclic form Trypanosoma brucei by epitope-tag organelle enrichment and SILAC proteomics.&quot; <i>J Proteome Res</i> <b>13</b>(6):2796&ndash;806; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24792668 24792668]; doi: [https://dx.doi.org/10.1021/pr401209w 10.1021/pr401209w]; GPMDB: [http://gpmdb.org/data/keyword/24792668 154].
+#Güther ML, Urbaniak MD, Tavendale A, Prescott A, Ferguson MA,  (2014) &quot;High-confidence glycosome proteome for procyclic form Trypanosoma brucei by epitope-tag organelle enrichment and SILAC proteomics.&quot; <i>J Proteome Res</i> <b>13</b>(6):2796&ndash;806; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24792668 24792668]; doi: [https://dx.doi.org/10.1021/pr401209w 10.1021/pr401209w]; GPMDB: [http://gpmdb.org/data/keyword/24792668 154].
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 #Tong J, Taylor P, Moran MF,  (2014) &quot;Proteomic analysis of the epidermal growth factor receptor (EGFR) interactome and post-translational modifications associated with receptor endocytosis in response to EGF and stress.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(7):1644&ndash;58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24797263 24797263]; doi: [https://dx.doi.org/10.1074/mcp.M114.038596 10.1074/mcp.M114.038596]; GPMDB: [http://gpmdb.org/data/keyword/24797263 69].
@@ Line 637: / Line 638: @@
 #Rowshanravan B, Woodcock SA, Botella JA, Kiermayer C, Schneuwly S, Hughes DA,  (2014) &quot;RasGAP mediates neuronal survival in Drosophila through direct regulation of Rab5-dependent endocytosis.&quot; <i>J Cell Sci</i> <b>127</b>(Pt 13):2849&ndash;61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24816559 24816559]; doi: [https://dx.doi.org/10.1242/jcs.139329 10.1242/jcs.139329]; GPMDB: [http://gpmdb.org/data/keyword/24816559 42].
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+#Siljamäki P, Varmanen P, Kankainen M, Sukura A, Savijoki K, Nyman TA,  (2014) &quot;Comparative exoprotein profiling of different Staphylococcus epidermidis strains reveals potential link between nonclassical protein export and virulence.&quot; <i>J Proteome Res</i> <b>13</b>(7):3249&ndash;61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24840314 24840314]; doi: [https://dx.doi.org/10.1021/pr500075j 10.1021/pr500075j]; GPMDB: [http://gpmdb.org/data/keyword/24840314 94].
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+#Köcher T, Pichler P, De Pra M, Rieux L, Swart R, Mechtler K,  (2014) &quot;Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up.&quot; <i>Proteomics</i> <b>14</b>(17-18):1999&ndash;2007; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24920484 24920484]; doi: [https://dx.doi.org/10.1002/pmic.201300418 10.1002/pmic.201300418]; GPMDB: [http://gpmdb.org/data/keyword/24920484 39].
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@@ Line 651: / Line 652: @@
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@@ Line 669: / Line 670: @@
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+#Aasebø E, Vaudel M, Mjaavatten O, Gausdal G, Van der Burgh A, Gjertsen BT, Døskeland 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, Guérin 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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@@ Line 679: / Line 680: @@
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+#Labas V, Grasseau I, Cahier K, Gargaros A, Harichaux G, Teixeira-Gomes AP, Alves S, Bourin M, Gérard 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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+#Perdomo D, Aït-Ammar N, Syan S, Sachse M, Jhingan GD, Guillén 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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+#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, Völker 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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+#Sharma K, D'Souza RC, Tyanova S, Schaab C, Wiśniewski JR, Cox J, Mann M,  (2014) &quot;Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling.&quot; <i>Cell Rep</i> <b>8</b>(5):1583&ndash;94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25159151 25159151]; doi: [https://dx.doi.org/10.1016/j.celrep.2014.07.036 10.1016/j.celrep.2014.07.036]; GPMDB: [http://gpmdb.org/data/keyword/25159151 276].
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+#Reinartz M, Raupach A, Kaisers W, Gödecke A,  (2014) &quot;AKT1 and AKT2 induce distinct phosphorylation patterns in HL-1 cardiac myocytes.&quot; <i>J Proteome Res</i> <b>13</b>(10):4232&ndash;45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25162660 25162660]; doi: [https://dx.doi.org/10.1021/pr500131g 10.1021/pr500131g]; GPMDB: [http://gpmdb.org/data/keyword/25162660 8].
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+#Dyrlund TF, Kirkegaard K, Poulsen ET, Sanggaard KW, Hindkjær JJ, Kjems J, Enghild JJ, Ingerslev HJ,  (2014) &quot;Unconditioned commercial embryo culture media contain a large variety of non-declared proteins: a comprehensive proteomics analysis.&quot; <i>Hum Reprod</i> <b>29</b>(11):2421&ndash;30; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25164020 25164020]; doi: [https://dx.doi.org/10.1093/humrep/deu220 10.1093/humrep/deu220]; GPMDB: [http://gpmdb.org/data/keyword/25164020 63].
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+#Liao BM, Raddatz K, Zhong L, Parker BL, Raftery MJ, Schmitz-Peiffer C,  (2014) &quot;Proteomic analysis of livers from fat-fed mice deficient in either PKCδ or PKCε identifies Htatip2 as a regulator of lipid metabolism.&quot; <i>Proteomics</i> <b>14</b>(21-22):2578&ndash;87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25175814 25175814]; doi: [https://dx.doi.org/10.1002/pmic.201400202 10.1002/pmic.201400202]; GPMDB: [http://gpmdb.org/data/keyword/25175814 222].
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+#Chocu S, Evrard B, Lavigne R, Rolland AD, Aubry F, Jégou B, Chalmel F, Pineau C,  (2014) &quot;Forty-four novel protein-coding loci discovered using a proteomics informed by transcriptomics (PIT) approach in rat male germ cells.&quot; <i>Biol Reprod</i> <b>91</b>(5):123; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25210130 25210130]; doi: [https://dx.doi.org/10.1095/biolreprod.114.122416 10.1095/biolreprod.114.122416]; GPMDB: [http://gpmdb.org/data/keyword/25210130 6].
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+#Negroni L, Taouji S, Arma D, Pallares-Lupon N, Leong K, Beausang LA, Latterich M, Bossé R, Balabaud C, Schmitter JM, Bioulac-Sage P, Zucman-Rossi J, Rosenbaum J, Chevet E,  (2014) &quot;Integrative quantitative proteomics unveils proteostasis imbalance in human hepatocellular carcinoma developed on nonfibrotic livers.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(12):3473&ndash;83; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25225353 25225353]; doi: [https://dx.doi.org/10.1074/mcp.M114.043174 10.1074/mcp.M114.043174]; GPMDB: [http://gpmdb.org/data/keyword/25225353 8].
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+#Wiśniewski JR, Hein MY, Cox J, Mann M,  (2014) &quot;A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards.&quot; <i>Mol Cell Proteomics</i> <b>13</b>(12):3497&ndash;506; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25225357 25225357]; doi: [https://dx.doi.org/10.1074/mcp.M113.037309 10.1074/mcp.M113.037309]; GPMDB: [http://gpmdb.org/data/keyword/25225357 69].
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+#Tape CJ, Worboys JD, Sinclair J, Gourlay R, Vogt J, McMahon KM, Trost M, Lauffenburger DA, Lamont DJ, Jørgensen C,  (2014) &quot;Reproducible automated phosphopeptide enrichment using magnetic TiO2 and Ti-IMAC.&quot; <i>Anal Chem</i> <b>86</b>(20):10296&ndash;302; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25233145 25233145]; doi: [https://dx.doi.org/10.1021/ac5025842 10.1021/ac5025842]; GPMDB: [http://gpmdb.org/data/keyword/25233145 103].
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@@ Line 723: / Line 724: @@
 #Yin X, Sakata K, Komatsu S,  (2014) &quot;Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress.&quot; <i>J Proteome Res</i> <b>13</b>(12):5618&ndash;34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25316100 25316100]; doi: [https://dx.doi.org/10.1021/pr500621c 10.1021/pr500621c]; GPMDB: [http://gpmdb.org/data/keyword/25316100 54].
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+#Herbst FA, Søndergaard MT, Kjeldal H, Stensballe A, Nielsen PH, Dueholm MS,  (2015) &quot;Major proteomic changes associated with amyloid-induced biofilm formation in Pseudomonas aeruginosa PAO1.&quot; <i>J Proteome Res</i> <b>14</b>(1):72&ndash;81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25317949 25317949]; doi: [https://dx.doi.org/10.1021/pr500938x 10.1021/pr500938x]; GPMDB: [http://gpmdb.org/data/keyword/25317949 282].
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+#Helgeland E, Breivik LE, Vaudel M, Svendsen ØS, Garberg H, Nordrehaug JE, Berven FS, Jonassen AK,  (2014) &quot;Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning--a word of caution.&quot; <i>PLoS One</i> <b>9</b>(10):e109279; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25333471 25333471]; doi: [https://dx.doi.org/10.1371/journal.pone.0109279 10.1371/journal.pone.0109279]; GPMDB: [http://gpmdb.org/data/keyword/25333471 146].
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@@ Line 739: / Line 740: @@
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+#Cubeñas-Potts C, Srikumar T, Lee C, Osula O, Subramonian D, Zhang XD, Cotter RJ, Raught B, Matunis MJ,  (2015) &quot;Identification of SUMO-2/3-modified proteins associated with mitotic chromosomes.&quot; <i>Proteomics</i> <b>15</b>(4):763&ndash;72; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25367092 25367092]; doi: [https://dx.doi.org/10.1002/pmic.201400400 10.1002/pmic.201400400]; GPMDB: [http://gpmdb.org/data/keyword/25367092 8].
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+#Pfeiffer MJ, Taher L, Drexler H, Suzuki Y, Makałowski W, Schwarzer C, Wang B, Fuellen G, Boiani M,  (2015) &quot;Differences in embryo quality are associated with differences in oocyte composition: a proteomic study in inbred mice.&quot; <i>Proteomics</i> <b>15</b>(4):675&ndash;87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25367296 25367296]; doi: [https://dx.doi.org/10.1002/pmic.201400334 10.1002/pmic.201400334]; GPMDB: [http://gpmdb.org/data/keyword/25367296 4].
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+#Götzke H, Muheim C, Altelaar AF, Heck AJ, Maddalo G, Daley DO,  (2015) &quot;Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(1):216&ndash;26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25403562 25403562]; doi: [https://dx.doi.org/10.1074/mcp.M114.043216 10.1074/mcp.M114.043216]; GPMDB: [http://gpmdb.org/data/keyword/25403562 9].
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+#Chawade A, Sandin M, Teleman J, Malmström J, Levander F,  (2015) &quot;Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.&quot; <i>J Proteome Res</i> <b>14</b>(2):676&ndash;87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25407311 25407311]; doi: [https://dx.doi.org/10.1021/pr500665j 10.1021/pr500665j]; GPMDB: [http://gpmdb.org/data/keyword/25407311 12].
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+#Gruber AR, Martin G, Müller P, Schmidt A, Gruber AJ, Gumienny R, Mittal N, Jayachandran R, Pieters J, Keller W, van Nimwegen E, Zavolan M,  (2014) &quot;Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells.&quot; <i>Nat Commun</i> <b>5</b>:5465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25413384 25413384]; doi: [https://dx.doi.org/10.1038/ncomms6465 10.1038/ncomms6465]; GPMDB: [http://gpmdb.org/data/keyword/25413384 13].
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-#WiÅ›niewski JR, Koepsell H, Gizak A, Rakus D,  (2015) &quot;Absolute protein quantification allows differentiation of cell-specific metabolic routes and functions.&quot; <i>Proteomics</i> <b>15</b>(7):1316&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25475432 25475432]; doi: [https://dx.doi.org/10.1002/pmic.201400456 10.1002/pmic.201400456]; GPMDB: [http://gpmdb.org/data/keyword/25475432 44].
+#Wiśniewski JR, Koepsell H, Gizak A, Rakus D,  (2015) &quot;Absolute protein quantification allows differentiation of cell-specific metabolic routes and functions.&quot; <i>Proteomics</i> <b>15</b>(7):1316&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25475432 25475432]; doi: [https://dx.doi.org/10.1002/pmic.201400456 10.1002/pmic.201400456]; GPMDB: [http://gpmdb.org/data/keyword/25475432 44].
 #Schnell G, Boeuf A, Jaulhac B, Boulanger N, Collin E, Barthel C, De Martino S, Ehret-Sabatier L,  (2015) &quot;Proteomic analysis of three Borrelia burgdorferi sensu lato native species and disseminating clones: relevance for Lyme vaccine design.&quot; <i>Proteomics</i> <b>15</b>(7):1280&ndash;90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25475896 25475896]; doi: [https://dx.doi.org/10.1002/pmic.201400177 10.1002/pmic.201400177]; GPMDB: [http://gpmdb.org/data/keyword/25475896 6].
 #Yang X, Liu F, Yan Y, Zhou T, Guo Y, Sun G, Zhou Z, Zhang W, Guo X, Sha J,  (2015) &quot;Proteomic analysis of N-glycosylation of human seminal plasma.&quot; <i>Proteomics</i> <b>15</b>(7):1255&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25476145 25476145]; doi: [https://dx.doi.org/10.1002/pmic.201400203 10.1002/pmic.201400203]; GPMDB: [http://gpmdb.org/data/keyword/25476145 3].
@@ Line 760: / Line 761: @@
 #Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R,  (2014) &quot;Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.&quot; <i>Mol Syst Biol</i> <b>10</b>:767; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25492886 25492886]; GPMDB: [http://gpmdb.org/data/keyword/25492886 108].
 #Selvam RM, Nithya R, Devi PN, Shree RS, Nila MV, Demonte NL, Thangavel C, Maheshwari JJ, Lalitha P, Prajna NV, Dharmalingam K,  (2015) &quot;Exoproteome of Aspergillus flavus corneal isolates and saprophytes: identification of proteoforms of an oversecreted alkaline protease.&quot; <i>J Proteomics</i> <b>115</b>:23&ndash;35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25497218 25497218]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.11.017 10.1016/j.jprot.2014.11.017]; GPMDB: [http://gpmdb.org/data/keyword/25497218 10].
-#Bergseng E, DÃ¸rum S, Arntzen MÃ˜, Nielsen M, NygÃ¥rd S, Buus S, de Souza GA, Sollid LM,  (2015) &quot;Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires.&quot; <i>Immunogenetics</i> <b>67</b>(2):73&ndash;84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25502872 25502872]; doi: [https://dx.doi.org/10.1007/s00251-014-0819-9 10.1007/s00251-014-0819-9]; GPMDB: [http://gpmdb.org/data/keyword/25502872 51].
+#Bergseng E, Dørum S, Arntzen MØ, Nielsen M, Nygård S, Buus S, de Souza GA, Sollid LM,  (2015) &quot;Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires.&quot; <i>Immunogenetics</i> <b>67</b>(2):73&ndash;84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25502872 25502872]; doi: [https://dx.doi.org/10.1007/s00251-014-0819-9 10.1007/s00251-014-0819-9]; GPMDB: [http://gpmdb.org/data/keyword/25502872 51].
-#Guo M, HÃ¤rtlova A, Dill BD, Prescott AR, GierliÅ„ski M, Trost M,  (2015) &quot;High-resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow derived macrophages.&quot; <i>Proteomics</i> <b>15</b>(18):3169&ndash;74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25504905 25504905]; doi: [https://dx.doi.org/10.1002/pmic.201400431 10.1002/pmic.201400431]; GPMDB: [http://gpmdb.org/data/keyword/25504905 6].
+#Guo M, Härtlova A, Dill BD, Prescott AR, Gierliński M, Trost M,  (2015) &quot;High-resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow derived macrophages.&quot; <i>Proteomics</i> <b>15</b>(18):3169&ndash;74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25504905 25504905]; doi: [https://dx.doi.org/10.1002/pmic.201400431 10.1002/pmic.201400431]; GPMDB: [http://gpmdb.org/data/keyword/25504905 6].
-#Gomes-Alves P, Serra M, Brito C, R-Borlado L, LÃ³pez JA, VÃ¡zquez J, Carrondo MJ, Bernad A, Alves PM,  (2015) &quot;Exploring analytical proteomics platforms toward the definition of human cardiac stem cells receptome.&quot; <i>Proteomics</i> <b>15</b>(7):1332&ndash;7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25504917 25504917]; doi: [https://dx.doi.org/10.1002/pmic.201400318 10.1002/pmic.201400318]; GPMDB: [http://gpmdb.org/data/keyword/25504917 2].
+#Gomes-Alves P, Serra M, Brito C, R-Borlado L, López JA, Vázquez J, Carrondo MJ, Bernad A, Alves PM,  (2015) &quot;Exploring analytical proteomics platforms toward the definition of human cardiac stem cells receptome.&quot; <i>Proteomics</i> <b>15</b>(7):1332&ndash;7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25504917 25504917]; doi: [https://dx.doi.org/10.1002/pmic.201400318 10.1002/pmic.201400318]; GPMDB: [http://gpmdb.org/data/keyword/25504917 2].
-#Baert Y, Stukenborg JB, Landreh M, De Kock J, JÃ¶rnvall H, SÃ¶der O, Goossens E,  (2015) &quot;Derivation and characterization of a cytocompatible scaffold from human testis.&quot; <i>Hum Reprod</i> <b>30</b>(2):256&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25505010 25505010]; doi: [https://dx.doi.org/10.1093/humrep/deu330 10.1093/humrep/deu330]; GPMDB: [http://gpmdb.org/data/keyword/25505010 1].
+#Baert Y, Stukenborg JB, Landreh M, De Kock J, Jörnvall H, Söder O, Goossens E,  (2015) &quot;Derivation and characterization of a cytocompatible scaffold from human testis.&quot; <i>Hum Reprod</i> <b>30</b>(2):256&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25505010 25505010]; doi: [https://dx.doi.org/10.1093/humrep/deu330 10.1093/humrep/deu330]; GPMDB: [http://gpmdb.org/data/keyword/25505010 1].
-#PelÃ¡ez-GarcÃa A, Barderas R, Batlle R, ViÃ±as-Castells R, BartolomÃ© RA, Torres S, Mendes M, Lopez-Lucendo M, Mazzolini R, Bonilla F, GarcÃa de Herreros A, Casal JI,  (2015) &quot;A proteomic analysis reveals that Snail regulates the expression of the nuclear orphan receptor Nuclear Receptor Subfamily 2 Group F Member 6 (Nr2f6) and interleukin 17 (IL-17) to inhibit adipocyte differentiation.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(2):303&ndash;15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25505127 25505127]; doi: [https://dx.doi.org/10.1074/mcp.M114.045328 10.1074/mcp.M114.045328]; GPMDB: [http://gpmdb.org/data/keyword/25505127 2].
+#Peláez-García A, Barderas R, Batlle R, Viñas-Castells R, Bartolomé RA, Torres S, Mendes M, Lopez-Lucendo M, Mazzolini R, Bonilla F, García de Herreros A, Casal JI,  (2015) &quot;A proteomic analysis reveals that Snail regulates the expression of the nuclear orphan receptor Nuclear Receptor Subfamily 2 Group F Member 6 (Nr2f6) and interleukin 17 (IL-17) to inhibit adipocyte differentiation.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(2):303&ndash;15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25505127 25505127]; doi: [https://dx.doi.org/10.1074/mcp.M114.045328 10.1074/mcp.M114.045328]; GPMDB: [http://gpmdb.org/data/keyword/25505127 2].
 #Gao L, Ge H, Huang X, Liu K, Zhang Y, Xu W, Wang Y,  (2015) &quot;Systematically ranking the tightness of membrane association for peripheral membrane proteins (PMPs).&quot; <i>Mol Cell Proteomics</i> <b>14</b>(2):340&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25505158 25505158]; doi: [https://dx.doi.org/10.1074/mcp.M114.044800 10.1074/mcp.M114.044800]; GPMDB: [http://gpmdb.org/data/keyword/25505158 24].
-#Low TY, Peng M, Magliozzi R, Mohammed S, Guardavaccaro D, Heck AJ,  (2014) &quot;A systems-wide screen identifies substrates of the SCFÎ²TrCP ubiquitin ligase.&quot; <i>Sci Signal</i> <b>7</b>(356):rs8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25515538 25515538]; doi: [https://dx.doi.org/10.1126/scisignal.2005882 10.1126/scisignal.2005882]; GPMDB: [http://gpmdb.org/data/keyword/25515538 120].
+#Low TY, Peng M, Magliozzi R, Mohammed S, Guardavaccaro D, Heck AJ,  (2014) &quot;A systems-wide screen identifies substrates of the SCFβTrCP ubiquitin ligase.&quot; <i>Sci Signal</i> <b>7</b>(356):rs8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25515538 25515538]; doi: [https://dx.doi.org/10.1126/scisignal.2005882 10.1126/scisignal.2005882]; GPMDB: [http://gpmdb.org/data/keyword/25515538 120].
 #Park JJ, Wang H, Gargouri M, Deshpande RR, Skepper JN, Holguin FO, Juergens MT, Shachar-Hill Y, Hicks LM, Gang DR,  (2015) &quot;The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis.&quot; <i>Plant J</i> <b>81</b>(4):611&ndash;24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25515814 25515814]; doi: [https://dx.doi.org/10.1111/tpj.12747 10.1111/tpj.12747]; GPMDB: [http://gpmdb.org/data/keyword/25515814 6].
 #Ferl RJ, Koh J, Denison F, Paul AL,  (2015) &quot;Spaceflight induces specific alterations in the proteomes of Arabidopsis.&quot; <i>Astrobiology</i> <b>15</b>(1):32&ndash;56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25517942 25517942]; doi: [https://dx.doi.org/10.1089/ast.2014.1210 10.1089/ast.2014.1210]; GPMDB: [http://gpmdb.org/data/keyword/25517942 15].
 #Mathias RA, Greco TM, Oberstein A, Budayeva HG, Chakrabarti R, Rowland EA, Kang Y, Shenk T, Cristea IM,  (2014) &quot;Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity.&quot; <i>Cell</i> <b>159</b>(7):1615&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25525879 25525879]; doi: [https://dx.doi.org/10.1016/j.cell.2014.11.046 10.1016/j.cell.2014.11.046]; GPMDB: [http://gpmdb.org/data/keyword/25525879 24].
-#Gueugneau M, Coudy-Gandilhon C, Gourbeyre O, Chambon C, Combaret L, Polge C, Taillandier D, Attaix D, Friguet B, Maier AB, Butler-Browne G, BÃ©chet D,  (2014) &quot;Proteomics of muscle chronological ageing in post-menopausal women.&quot; <i>BMC Genomics</i> <b>15</b>:1165; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25532418 25532418]; doi: [https://dx.doi.org/10.1186/1471-2164-15-1165 10.1186/1471-2164-15-1165]; GPMDB: [http://gpmdb.org/data/keyword/25532418 98].
+#Gueugneau M, Coudy-Gandilhon C, Gourbeyre O, Chambon C, Combaret L, Polge C, Taillandier D, Attaix D, Friguet B, Maier AB, Butler-Browne G, Béchet D,  (2014) &quot;Proteomics of muscle chronological ageing in post-menopausal women.&quot; <i>BMC Genomics</i> <b>15</b>:1165; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25532418 25532418]; doi: [https://dx.doi.org/10.1186/1471-2164-15-1165 10.1186/1471-2164-15-1165]; GPMDB: [http://gpmdb.org/data/keyword/25532418 98].
-#Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, GuÃ©nolÃ© A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM,  (2015) &quot;Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.&quot; <i>Mol Cell</i> <b>57</b>(2):273&ndash;89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25533186 25533186]; doi: [https://dx.doi.org/10.1016/j.molcel.2014.11.016 10.1016/j.molcel.2014.11.016]; GPMDB: [http://gpmdb.org/data/keyword/25533186 12].
+#Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM,  (2015) &quot;Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling.&quot; <i>Mol Cell</i> <b>57</b>(2):273&ndash;89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25533186 25533186]; doi: [https://dx.doi.org/10.1016/j.molcel.2014.11.016 10.1016/j.molcel.2014.11.016]; GPMDB: [http://gpmdb.org/data/keyword/25533186 12].
-#Paster W, Bruger AM, Katsch K, GrÃ©goire C, Roncagalli R, Fu G, Gascoigne NR, Nika K, Cohnen A, Feller SM, Simister PC, Molder KC, Cordoba SP, Dushek O, Malissen B, Acuto O,  (2015) &quot;A THEMIS:SHP1 complex promotes T-cell survival.&quot; <i>EMBO J</i> <b>34</b>(3):393&ndash;409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25535246 25535246]; doi: [https://dx.doi.org/10.15252/embj.201387725 10.15252/embj.201387725]; GPMDB: [http://gpmdb.org/data/keyword/25535246 15].
+#Paster W, Bruger AM, Katsch K, Grégoire C, Roncagalli R, Fu G, Gascoigne NR, Nika K, Cohnen A, Feller SM, Simister PC, Molder KC, Cordoba SP, Dushek O, Malissen B, Acuto O,  (2015) &quot;A THEMIS:SHP1 complex promotes T-cell survival.&quot; <i>EMBO J</i> <b>34</b>(3):393&ndash;409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25535246 25535246]; doi: [https://dx.doi.org/10.15252/embj.201387725 10.15252/embj.201387725]; GPMDB: [http://gpmdb.org/data/keyword/25535246 15].
 #Hubner NC, Nguyen LN, Hornig NC, Stunnenberg HG,  (2015) &quot;A quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood.&quot; <i>J Proteome Res</i> <b>14</b>(2):1315&ndash;29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25546135 25546135]; doi: [https://dx.doi.org/10.1021/pr5009515 10.1021/pr5009515]; GPMDB: [http://gpmdb.org/data/keyword/25546135 82].
 #Chang HY, Li MH, Huang TC, Hsu CL, Tsai SR, Lee SC, Huang HC, Juan HF,  (2015) &quot;Quantitative proteomics reveals middle infrared radiation-interfered networks in breast cancer cells.&quot; <i>J Proteome Res</i> <b>14</b>(2):1250&ndash;62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25556991 25556991]; doi: [https://dx.doi.org/10.1021/pr5011873 10.1021/pr5011873]; GPMDB: [http://gpmdb.org/data/keyword/25556991 1].
-#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, Ã–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].
+#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, Öhlund 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].
 #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].
 #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].
 #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].
 #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].
-#Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ãœ, KÃµks 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].
+#Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ü, Kõks 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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 #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].
@@ Line 786: / Line 787: @@
 #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].
 #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 naïve, activated, effector, and memory CD8⁺ 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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+#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 Iβ 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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+#Médard 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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+#Jacques S, Ghesquière 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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+#González-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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+#Štalekar 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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+#Schölz 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, Völker 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, Sigurðsson 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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+#Martin-Perez M, Villén 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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@@ Line 823: / Line 824: @@
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+#Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E, Genetic and Environmental Risk for Alzheimer’s Disease GERAD1 Consortium, Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M,  (2015) &quot;Quantitative interaction proteomics of neurodegenerative disease proteins.&quot; <i>Cell Rep</i> <b>11</b>(7):1134&ndash;46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25959826 25959826]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.04.030 10.1016/j.celrep.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25959826 122].
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+#Koch H, Busto ME, Kramer K, Médard G, Kuster B,  (2015) &quot;Chemical Proteomics Uncovers EPHA2 as a Mechanism of Acquired Resistance to Small Molecule EGFR Kinase Inhibition.&quot; <i>J Proteome Res</i> <b>14</b>(6):2617&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963923 25963923]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00161 10.1021/acs.jproteome.5b00161]; GPMDB: [http://gpmdb.org/data/keyword/25963923 18].
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@@ Line 856: / Line 857: @@
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+#Dinets A, Pernemalm M, Kjellin H, Sviatoha V, Sofiadis A, Juhlin CC, Zedenius J, Larsson C, Lehtiö J, Höög A,  (2015) &quot;Differential protein expression profiles of cyst fluid from papillary thyroid carcinoma and benign thyroid lesions.&quot; <i>PLoS One</i> <b>10</b>(5):e0126472; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25978681 25978681]; doi: [https://dx.doi.org/10.1371/journal.pone.0126472 10.1371/journal.pone.0126472]; GPMDB: [http://gpmdb.org/data/keyword/25978681 2].
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+#Campos A, Díaz R, Martínez-Bartolomé S, Sierra J, Gallardo O, Sabidó E, López-Lucendo M, Ignacio Casal J, Pasquarello C, Scherl A, Chiva C, Borras E, Odena A, Elortza F, Azkargorta M, Ibarrola N, Canals F, Albar JP, Oliveira E,  (2015) &quot;Multicenter experiment for quality control of peptide-centric LC-MS/MS analysis - A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers.&quot; <i>J Proteomics</i> <b>127</b>(Pt B):264&ndash;74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25982386 25982386]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.012 10.1016/j.jprot.2015.05.012]; GPMDB: [http://gpmdb.org/data/keyword/25982386 112].
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+#Bennike TB, Carlsen TG, Ellingsen T, Bonderup OK, Glerup H, Bøgsted M, Christiansen G, Birkelund S, Stensballe A, Andersen V,  (2015) &quot;Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies.&quot; <i>Inflamm Bowel Dis</i> <b>21</b>(9):2052&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25993694 25993694]; doi: [https://dx.doi.org/10.1097/MIB.0000000000000460 10.1097/MIB.0000000000000460]; GPMDB: [http://gpmdb.org/data/keyword/25993694 60].
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@@ Line 865: / Line 866: @@
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+#Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS,  (2015) &quot;Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells.&quot; <i>Stem Cells</i> <b>33</b>(9):2712&ndash;25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26059426 26059426]; doi: [https://dx.doi.org/10.1002/stem.2067 10.1002/stem.2067]; GPMDB: [http://gpmdb.org/data/keyword/26059426 7].
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+#Wiśniewski JR, Gizak A, Rakus D,  (2015) &quot;Integrating Proteomics and Enzyme Kinetics Reveals Tissue-Specific Types of the Glycolytic and Gluconeogenic Pathways.&quot; <i>J Proteome Res</i> <b>14</b>(8):3263&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26080680 26080680]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00276 10.1021/acs.jproteome.5b00276]; GPMDB: [http://gpmdb.org/data/keyword/26080680 18].
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+#Barco RA, Emerson D, Sylvan JB, Orcutt BN, Jacobson Meyers ME, Ramírez GA, Zhong JD, Edwards KJ,  (2015) &quot;New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph.&quot; <i>Appl Environ Microbiol</i> <b>81</b>(17):5927&ndash;37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26092463 26092463]; doi: [https://dx.doi.org/10.1128/AEM.01374-15 10.1128/AEM.01374-15]; GPMDB: [http://gpmdb.org/data/keyword/26092463 28].
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+#Díez P, Droste C, Dégano RM, González-Muñoz M, Ibarrola N, Pérez-Andrés 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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+#Haurogné 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, Brümmer 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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+#Wiśniewski JR, Duś-Szachniewicz K, Ostasiewicz P, Ziółkowski 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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+#Toledo A, Pérez 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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@@ Line 923: / Line 924: @@
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+#Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast ÁM, 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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+#Shrivastava AN, Redeker V, Fritz N, Pieri L, Almeida LG, Spolidoro M, Liebmann T, Bousset L, Renner M, Léna C, Aperia A, Melki R, Triller A,  (2015) &quot;α-synuclein assemblies sequester neuronal α3-Na+/K+-ATPase and impair Na+ gradient.&quot; <i>EMBO J</i> <b>34</b>(19):2408&ndash;23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26323479 26323479]; doi: [https://dx.doi.org/10.15252/embj.201591397 10.15252/embj.201591397]; GPMDB: [http://gpmdb.org/data/keyword/26323479 23].
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@@ Line 938: / Line 939: @@
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+#Ruprecht B, Zecha J, Heinzlmeir S, Médard G, Lemeer S, Kuster B,  (2015) &quot;Evaluation of Kinase Activity Profiling Using Chemical Proteomics.&quot; <i>ACS Chem Biol</i> <b>10</b>(12):2743&ndash;52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378887 26378887]; doi: [https://dx.doi.org/10.1021/acschembio.5b00616 10.1021/acschembio.5b00616]; GPMDB: [http://gpmdb.org/data/keyword/26378887 94].
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+#Kieselbach T, Zijnge V, Granström E, Oscarsson J,  (2015) &quot;Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles.&quot; <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5].
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+#Glatter T, Ahrné E, Schmidt A,  (2015) &quot;Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells.&quot; <i>J Proteome Res</i> <b>14</b>(11):4472&ndash;85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 493].
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@@ Line 950: / Line 951: @@
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+#Zhang H, Ramakrishnan SK, Triner D, Centofanti B, Maitra D, Győrffy B, Sebolt-Leopold JS, Dame MK, Varani J, Brenner DE, Fearon ER, Omary MB, Shah YM,  (2015) &quot;Tumor-selective proteotoxicity of verteporfin inhibits colon cancer progression independently of YAP1.&quot; <i>Sci Signal</i> <b>8</b>(397):ra98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26443705 26443705]; doi: [https://dx.doi.org/10.1126/scisignal.aac5418 10.1126/scisignal.aac5418]; GPMDB: [http://gpmdb.org/data/keyword/26443705 2].
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@@ Line 963: / Line 964: @@
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+#Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB,  (2015) &quot;A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.&quot; <i>PLoS One</i> <b>10</b>(11):e0142162; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26539827 26539827]; doi: [https://dx.doi.org/10.1371/journal.pone.0142162 10.1371/journal.pone.0142162]; GPMDB: [http://gpmdb.org/data/keyword/26539827 50].
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@@ Line 971: / Line 972: @@
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+#Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H,  (2016) &quot;Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides.&quot; <i>Nat Biotechnol</i> <b>34</b>(1):84&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55].
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@@ Line 981: / Line 982: @@
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@@ Line 987: / Line 988: @@
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+#Völker-Albert MC, Pusch MC, Fedisch A, Schilcher P, Schmidt A, Imhof A,  (2016) &quot;A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(3):945&ndash;59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26811354 26811354]; doi: [https://dx.doi.org/10.1074/mcp.M115.053553 10.1074/mcp.M115.053553]; GPMDB: [http://gpmdb.org/data/keyword/26811354 12].
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+#Kristensen TN, Kjeldal H, Schou MF, Nielsen JL,  (2016) &quot;Proteomic data reveals a physiological basis for costs and benefits associated with thermal acclimation.&quot; <i>J Exp Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9].
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@@ Line 1,044: / Line 1,047: @@
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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 β-oxidation pathway in HepG2 cells.&quot; <i>Amino Acids</i>; 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'Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, Böhm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingmüller 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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@@ Line 1,053: / Line 1,056: @@
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+#Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry 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, Jørgensen 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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@@ Line 1,067: / Line 1,070: @@
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