GPMDB Data Sources

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Revision as of 21:14, 10 June 2020

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;
JPOST;
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Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.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 be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.

CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.

Data from publications

The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of June 7, 2020.

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.
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Aubert G, Martin OJ, Horton JL, Lai L, Vega RB, Leone TC, Koves T, Gardell SJ, Krüger M, Hoppel CL, Lewandowski ED, Crawford PA, Muoio DM, Kelly DP, (2016) "The Failing Heart Relies on Ketone Bodies as a Fuel." Circulation 133(8):698–705; PMID: 26819376; doi: 10.1161/CIRCULATIONAHA.115.017355; GPMDB: 115.
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Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE, (2016) "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." Cancer Cell 29(2):214–28; PMID: 26832662; doi: 10.1016/j.ccell.2015.12.011; GPMDB: 72.
Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ, (2016) "Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition." J Cell Biol 212(3):349–64; PMID: 26833789; doi: 10.1083/jcb.201508080; GPMDB: 9.
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Tong M, Kleffmann T, Pradhan S, Johansson CL, DeSousa J, Stone PR, James JL, Chen Q, Chamley LW, (2016) "Proteomic characterization of macro-, micro- and nano-extracellular vesicles derived from the same first trimester placenta: relevance for feto-maternal communication." Hum Reprod 31(4):687–99; PMID: 26839151; doi: 10.1093/humrep/dew004; GPMDB: 3.
Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA, (2016) "PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis." Elife 5:e13292; PMID: 26839287; doi: 10.7554/eLife.13292; GPMDB: 9.
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Meierhofer D, Halbach M, Şen NE, Gispert S, Auburger G, (2016) "Ataxin-2 (Atxn2)-Knock-Out Mice Show Branched Chain Amino Acids and Fatty Acids Pathway Alterations." Mol Cell Proteomics 15(5):1728–39; PMID: 26850065; doi: 10.1074/mcp.M115.056770; GPMDB: 48.
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Billing AM, Ben Hamidane H, Dib SS, Cotton RJ, Bhagwat AM, Kumar P, Hayat S, Yousri NA, Goswami N, Suhre K, Rafii A, Graumann J, (2016) "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.
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Schneider RK, Schenone M, Ferreira MV, Kramann R, Joyce CE, Hartigan C, Beier F, Brümmendorf TH, Germing U, Platzbecker U, Büsche G, Knüchel R, Chen MC, Waters CS, Chen E, Chu LP, Novina CD, Lindsley RC, Carr SA, Ebert BL, (2016) "Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8 and S100A9." Nat Med 22(3):288–97; PMID: 26878232; doi: 10.1038/nm.4047; GPMDB: 1.
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Hiramatsu K, Yoshino K, Serada S, Yoshihara K, Hori Y, Fujimoto M, Matsuzaki S, Egawa-Takata T, Kobayashi E, Ueda Y, Morii E, Enomoto T, Naka T, Kimura T, (2016) "Similar protein expression profiles of ovarian and endometrial high-grade serous carcinomas." Br J Cancer 114(5):554–61; PMID: 26889980; doi: 10.1038/bjc.2016.27; GPMDB: 6.
Adav SS, Gallart-Palau X, Tan KH, Lim SK, Tam JP, Sze SK, (2016) "Dementia-linked amyloidosis is associated with brain protein deamidation as revealed by proteomic profiling of human brain tissues." Mol Brain 9:20; PMID: 26892330; doi: 10.1186/s13041-016-0200-z; GPMDB: 4.
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Zilkenat S, Franz-Wachtel M, Stierhof YD, Galán 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 15(5):1598–609; 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 26(5):660–9; PMID: 26912414; doi: 10.1101/gr.198911.115; GPMDB: 26.
Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder E, Carr SA, Jaffe JD, (2016) "Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes." Mol Cell Proteomics 15(5):1622–41; PMID: 26912667; doi: 10.1074/mcp.M116.058354; GPMDB: 4.
Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M, (2016) "In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics." Mol Cell Proteomics 15(5):1642–57; 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.
Xu B, Gao Y, Zhan S, Xiong F, Qiu W, Qian X, Wang T, Wang N, Zhang D, Yang Q, Wang R, Bao X, Dou W, Tian R, Meng S, Gai WP, Huang Y, Yan XX, Ge W, Ma C, (2016) "Quantitative protein profiling of hippocampus during human aging." Neurobiol Aging 39:46–56; PMID: 26923401; doi: 10.1016/j.neurobiolaging.2015.11.029; GPMDB: 20.
Reddy RJ, Gajadhar AS, Swenson EJ, Rothenberg DA, Curran TG, White FM, (2016) "Early signaling dynamics of the epidermal growth factor receptor." Proc Natl Acad Sci U S A 113(11):3114–9; PMID: 26929352; doi: 10.1073/pnas.1521288113; GPMDB: 30.
Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Müller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G, (2016) "An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client." Mol Cell Proteomics 15(3):1139–50; PMID: 26933192; doi: 10.1074/mcp.O115.055350 ; GPMDB: 16.
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Ly A, Merl-Pham J, Priller M, Gruhn F, Senninger N, Ueffing M, Hauck SM, (2016) "Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model." J Proteome Res 15(4):1350–9; PMID: 26939627; doi: 10.1021/acs.jproteome.6b00111; GPMDB: 24.
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 27(10):3079–3092; 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 Caenorhabditis elegans." Mol Cell Proteomics 15(5):1670–80; PMID: 26944343; doi: 10.1074/mcp.M115.052548; GPMDB: 12.
Zhang T, Shen S, Qu J, Ghaemmaghami S, (2016) "Global Analysis of Cellular Protein Flux Quantifies the Selectivity of Basal Autophagy." Cell Rep 14(10):2426–39; PMID: 26947064; doi: 10.1016/j.celrep.2016.02.040; GPMDB: 13.
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 10(5):554–63; PMID: 26947931; doi: 10.1002/prca.201500136; GPMDB: 1.
Adewole OO, Erhabor GE, Adewole TO, Ojo AO, Oshokoya H, Wolfe LM, Prenni JE, (2016) "Proteomic profiling of eccrine sweat reveals its potential as a diagnostic biofluid for active tuberculosis." Proteomics Clin Appl 10(5):547–53; 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 16:195; PMID: 26951071; doi: 10.1186/s12885-016-2193-5; GPMDB: 5.
De Marchi T, Kuhn E, Dekker LJ, Stingl C, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Luider TM, Foekens JA, Martens JW, Carr SA, Umar A, (2016) "Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera." J Proteome Res 15(4):1230–42; PMID: 26958999; doi: 10.1021/acs.jproteome.5b01119; GPMDB: 78.
Jo DH, Bae J, Chae S, Kim JH, Han JH, Hwang D, Lee SW, Kim JH, (2016) "Quantitative Proteomics Reveals β2 Integrin-mediated Cytoskeletal Rearrangement in Vascular Endothelial Growth Factor (VEGF)-induced Retinal Vascular Hyperpermeability." Mol Cell Proteomics 15(5):1681–91; PMID: 26969716; doi: 10.1074/mcp.M115.053249; GPMDB: 72.
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Gallart-Palau X, Lee BS, Adav SS, Qian J, Serra A, Park JE, Lai MK, Chen CP, Kalaria RN, Sze SK, (2016) "Gender differences in white matter pathology and mitochondrial dysfunction in Alzheimer's disease with cerebrovascular disease." Mol Brain 9:27; PMID: 26983404; doi: 10.1186/s13041-016-0205-7; GPMDB: 10.
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Danda R, Ganapathy K, Sathe G, Madugundu AK, Ramachandran S, Krishnan UM, Khetan V, Rishi P, Keshava Prasad TS, Pandey A, Krishnakumar S, Gowda H, Elchuri SV, (2016) "Proteomic profiling of retinoblastoma by high resolution mass spectrometry." Clin Proteomics 13:29; PMID: 27799869; doi: 10.1186/s12014-016-9128-7; GPMDB: 1.
Fahrmann JF, Grapov D, Phinney BS, Stroble C, DeFelice BC, Rom W, Gandara DR, Zhang Y, Fiehn O, Pass H, Miyamoto S, (2016) "Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival." Clin Proteomics 13:31; PMID: 27799870; doi: 10.1186/s12014-016-9132-y; GPMDB: 234.
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Borziak K, Álvarez-Fernández A, L Karr T, Pizzari T, Dorus S, (2016) "The Seminal fluid proteome of the polyandrous Red junglefowl offers insights into the molecular basis of fertility, reproductive ageing and domestication." Sci Rep 6:35864; PMID: 27804984; doi: 10.1038/srep35864; GPMDB: 144.
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Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." J Cell Sci 129(24):4466–4479; PMID: 27807006; doi: 10.1242/jcs.198614; GPMDB: 18.
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Wang J, Mauvoisin D, Martin E, Atger F, Galindo AN, Dayon L, Sizzano F, Palini A, Kussmann M, Waridel P, Quadroni M, Dulić V, Naef F, Gachon F, (2016) "Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver." Cell Metab; PMID: 27818260; doi: 10.1016/j.cmet.2016.10.003; GPMDB: 28.
Kogel U, Titz B, Schlage WK, Nury C, Martin F, Oviedo A, Lebrun S, Elamin A, Guedj E, Trivedi K, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J, (2016) "Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke." Regul Toxicol Pharmacol 81 Suppl 2:S123–S138; PMID: 27818347; doi: 10.1016/j.yrtph.2016.11.001; GPMDB: 36.
Hansen RK, Mund A, Poulsen SL, Sandoval M, Klement K, Tsouroula K, Tollenaere MA, Räschle M, Soria R, Offermanns S, Worzfeld T, Grosse R, Brandt DT, Rozell B, Mann M, Cole F, Soutoglou E, Goodarzi AA, Daniel JA, Mailand N, Bekker-Jensen S, (2016) "SCAI promotes DNA double-strand break repair in distinct chromosomal contexts." Nat Cell Biol 18(12):1357–1366; PMID: 27820601; doi: 10.1038/ncb3436; GPMDB: 12.
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Mardakheh FK, Sailem HZ, Kümper S, Tape CJ, McCully RR, Paul A, Anjomani-Virmouni S, Jørgensen C, Poulogiannis G, Marshall CJ, Bakal C, (2016) "Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)." Mol Biosyst 13(1):92–105; PMID: 27824369; doi: 10.1039/c6mb00701e; GPMDB: 16.
Warpman Berglund U, Sanjiv K, Gad H, Kalderén C, Koolmeister T, Pham T, Gokturk C, Jafari R, Maddalo G, Seashore-Ludlow B, Chernobrovkin A, Manoilov A, Pateras IS, Rasti A, Jemth AS, Almlöf I, Loseva O, Visnes T, Einarsdottir BO, Gaugaz FZ, Saleh A, Platzack B, Wallner OA, Vallin KS, Henriksson M, Wakchaure P, Borhade S, Herr P, Kallberg Y, Baranczewski P, Homan EJ, Wiita E, Nagpal V, Meijer T, Schipper N, Rudd SG, Bräutigam L, Lindqvist A, Filppula A, Lee TC, Artursson P, Nilsson JA, Gorgoulis VG, Lehtiö J, Zubarev RA, Scobie M, Helleday T, (2016) "Validation and development of MTH1 inhibitors for treatment of cancer." Ann Oncol 27(12):2275–2283; PMID: 27827301; doi: 10.1093/annonc/mdw429; GPMDB: 4.
Liu Y, Sellegounder D, Sun J, (2016) "Neuronal GPCR OCTR-1 regulates innate immunity by controlling protein synthesis in Caenorhabditis elegans." Sci Rep 6:36832; PMID: 27833098; doi: 10.1038/srep36832; GPMDB: 20.
Doll S, Urisman A, Oses-Prieto JA, Arnott D, Burlingame AL, (2016) "Quantitative proteomics reveals fundamental regulatory differences in oncogenic HRAS and IDH1 driven astrocytoma." Mol Cell Proteomics; PMID: 27834733; doi: 10.1074/mcp.M116.063883; GPMDB: 14.
Valdés A, García-Cañas V, Artemenko KA, Simó C, Bergquist J, Cifuentes A, (2016) "Nano-liquid chromatography-orbitrap MS -based quantitative proteomics reveals differences between the mechanisms of action of carnosic acid and carnosol in colon cancer cells." Mol Cell Proteomics; PMID: 27834734; doi: 10.1074/mcp.M116.061481; GPMDB: 54.
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Eisenberg T, Abdellatif M, Schroeder S, Primessnig U, Stekovic S, Pendl T, Harger A, Schipke J, Zimmermann A, Schmidt A, Tong M, Ruckenstuhl C, Dammbrueck C, Gross AS, Herbst V, Magnes C, Trausinger G, Narath S, Meinitzer A, Hu Z, Kirsch A, Eller K, Carmona-Gutierrez D, Büttner S, Pietrocola F, Knittelfelder O, Schrepfer E, Rockenfeller P, Simonini C, Rahn A, Horsch M, Moreth K, Beckers J, Fuchs H, Gailus-Durner V, Neff F, Janik D, Rathkolb B, Rozman J, de Angelis MH, Moustafa T, Haemmerle G, Mayr M, Willeit P, von Frieling-Salewsky M, Pieske B, Scorrano L, Pieber T, Pechlaner R, Willeit J, Sigrist SJ, Linke WA, Mühlfeld C, Sadoshima J, Dengjel J, Kiechl S, Kroemer G, Sedej S, Madeo F, (2016) "Cardioprotection and lifespan extension by the natural polyamine spermidine." Nat Med 22(12):1428–1438; PMID: 27841876; doi: 10.1038/nm.4222; GPMDB: 9.
Villoria MT, Ramos F, Dueñas E, Faull P, Cutillas PR, Clemente-Blanco A, (2017) "Stabilization of the metaphase spindle by Cdc14 is required for recombinational DNA repair." EMBO J 36(1):79–101; PMID: 27852625; doi: 10.15252/embj.201593540; GPMDB: 12.
Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR, (2016) "Multiparameter functional diversity of human C2H2 zinc finger proteins." Genome Res 26(12):1742–1752; PMID: 27852650; doi: 10.1101/gr.209643.116; GPMDB: 224.
Beringer M, Pisano P, Di Carlo V, Blanco E, Chammas P, Vizán P, Gutiérrez A, Aranda S, Payer B, Wierer M, Di Croce L, (2016) "EPOP Functionally Links Elongin and Polycomb in Pluripotent Stem Cells." Mol Cell 64(4):645–658; PMID: 27863225; doi: 10.1016/j.molcel.2016.10.018; GPMDB: 12.
Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." Nat Commun 7:13404; PMID: 27869121; doi: 10.1038/ncomms13404; GPMDB: 138.
Wallace PW, Haernvall K, Ribitsch D, Zitzenbacher S, Schittmayer M, Steinkellner G, Gruber K, Guebitz GM, Birner-Gruenberger R, (2016) "PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes." Appl Microbiol Biotechnol; PMID: 27872998; doi: 10.1007/s00253-016-7992-8; GPMDB: 28.
Muqaku B, Eisninger M, Meier SM, Tahir A, Prokop T, Haferkamp S, Slany A, Reichle A, Gerner C, (2016) "Multi-omics analysis of serum samples demonstrates reprogramming of organ functions via systemic calcium mobilization and platelet activation in metastatic melanoma." Mol Cell Proteomics; PMID: 27879288; doi: 10.1074/mcp.M116.063313; GPMDB: 18.
St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." Cell Rep 17(9):2488–2501; PMID: 27880917; doi: 10.1016/j.celrep.2016.10.078; GPMDB: 315.
Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." Nat Commun 7:13595; PMID: 27882920; doi: 10.1038/ncomms13595; GPMDB: 9.
Mossina A, Lukas C, Merl-Pham J, Uhl FE, Mutze K, Schamberger A, Staab-Weijnitz C, Jia J, Yildirim AÖ, Königshoff M, Hauck SM, Eickelberg O, Meiners S, (2017) "Cigarette smoke alters the secretome of lung epithelial cells." Proteomics 17(1-2):; PMID: 27891773; doi: 10.1002/pmic.201600243; GPMDB: 24.
Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." Oncotarget 7(52):86999–87015; PMID: 27894104; doi: 10.18632/oncotarget.13569; GPMDB: 898.
Gonneaud A, Jones C, Turgeon N, Lévesque D, Asselin C, Boudreau F, Boisvert FM, (2016) "A SILAC-Based Method for Quantitative Proteomic Analysis of Intestinal Organoids." Sci Rep 6:38195; PMID: 27901089; doi: 10.1038/srep38195; GPMDB: 38.
Song L, Wang F, Dong Z, Hua X, Xia Q, (2017) "Label-free quantitative phosphoproteomic profiling of cellular response induced by an insect cytokine paralytic peptide." J Proteomics 154:49–58; PMID: 27903465; doi: 10.1016/j.jprot.2016.11.018; GPMDB: 6.
Sundberg M, Strage EM, Bergquist J, Holst BS, Ramström M, (2016) "Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry." PLoS One 11(12):e0167138; PMID: 27907059; doi: 10.1371/journal.pone.0167138; GPMDB: 3.
Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT, (2016) "A proteomic approach to analyse the aspirin-mediated lysine acetylome." Mol Cell Proteomics; PMID: 27913581; doi: 10.1074/mcp.O116.065219; GPMDB: 40.
Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." Neuron 92(6):1220–1237; PMID: 27916455; doi: 10.1016/j.neuron.2016.10.064; GPMDB: 377.
Tiberti N, Latham SL, Bush S, Cohen A, Opoka RO, John CC, Juillard A, Grau GE, Combes V, (2016) "Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content." Sci Rep 6:37871; PMID: 27917875; doi: 10.1038/srep37871; GPMDB: 4.
Tedeschi G, Albani E, Borroni EM, Parini V, Brucculeri AM, Maffioli E, Negri A, Nonnis S, Maccarrone M, Levi-Setti PE, (2016) "Proteomic profile of maternal-aged blastocoel fluid suggests a novel role for ubiquitin system in blastocyst quality." J Assist Reprod Genet; PMID: 27924460; doi: 10.1007/s10815-016-0842-x; GPMDB: 10.
Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM, (2016) "Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition." J Proteome Res 15(12):4476–4489; PMID: 27934295; doi: 10.1021/acs.jproteome.6b00613; GPMDB: 18.
Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." J Proteome Res; PMID: 27959563; doi: 10.1021/acs.jproteome.6b00834; GPMDB: 6.
Seidel G, Meierhofer D, Şen NE, Guenther A, Krobitsch S, Auburger G, (2016) "Quantitative Global Proteomics of Yeast PBP1 Deletion Mutants and Their Stress Responses Identifies Glucose Metabolism, Mitochondrial, and Stress Granule Changes." J Proteome Res; PMID: 27966978; doi: 10.1021/acs.jproteome.6b00647; GPMDB: 27.
Dauden MI, Kosinski J, Kolaj-Robin O, Desfosses A, Ori A, Faux C, Hoffmann NA, Onuma OF, Breunig KD, Beck M, Sachse C, Séraphin B, Glatt S, Müller CW, (2016) "Architecture of the yeast Elongator complex." EMBO Rep; PMID: 27974378; doi: 10.15252/embr.201643353; GPMDB: 44.
Herfs M, Longuespée R, Quick CM, Roncarati P, Suarez-Carmona M, Hubert P, Lebeau A, Bruyere D, Mazzucchelli G, Smargiasso N, Baiwir D, Lai K, Dunn A, Obregon F, Yang EJ, De Pauw E, Crum CP, Delvenne P, (2016) "Proteomic signatures reveal a dualistic and clinically relevant classification of anal canal carcinoma." J Pathol; PMID: 27976366; doi: 10.1002/path.4858; GPMDB: 60.
Zhang S, Weng T, Cheruba E, Guo T, Chan H, Sze SK, Koh CG, (2016) "Phosphatase POPX2 Exhibits Dual Regulatory Functions in Cancer Metastasis." J Proteome Res; PMID: 27976581; doi: 10.1021/acs.jproteome.6b00748; GPMDB: 60.
Schunter AJ, Yue X, Hummon AB, (2016) "Phosphoproteomics of colon cancer metastasis: comparative mass spectrometric analysis of the isogenic primary and metastatic cell lines SW480 and SW620." Anal Bioanal Chem; PMID: 27987026; doi: 10.1007/s00216-016-0125-5; GPMDB: 35.
Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O, (2016) "ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments." J Proteome Res; PMID: 27990823; doi: 10.1021/acs.jproteome.6b00881; GPMDB: 12.
Bertile F, Fouillen L, Wasselin T, Maes P, Le Maho Y, Van Dorsselaer A, Raclot T, (2016) "The Safety Limits Of An Extended Fast: Lessons from a Non-Model Organism." Sci Rep 6:39008; PMID: 27991520; doi: 10.1038/srep39008; GPMDB: 194.
Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC, (2016) "VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis." Mol Cell Proteomics; PMID: 28007913; doi: 10.1074/mcp.M116.064428; GPMDB: 89.
Geyer PE, Wewer Albrechtsen NJ, Tyanova S, Grassl N, Iepsen EW, Lundgren J, Madsbad S, Holst JJ, Torekov SS, Mann M, (2016) "Proteomics reveals the effects of sustained weight loss on the human plasma proteome." Mol Syst Biol 12(12):901; PMID: 28007936; GPMDB: 1145.
Reimann L, Wiese H, Leber Y, Schwäble AN, Fricke AL, Rohland A, Knapp B, Peikert CD, Drepper F, van der Ven PF, Radziwill G, Fürst DO, Warscheid B, (2016) "Myofibrillar Z-discs are a protein phosphorylation hot spot with PKC α modulating protein dynamics." Mol Cell Proteomics; PMID: 28028127; doi: 10.1074/mcp.M116.065425; GPMDB: 278.
Rougemont B, Bontemps Gallo S, Ayciriex S, Carriere R, Hondermarck H, Lacroix JM, Le Blanc JC, Lemoine J, (2016) "Scout-MRM: multiplexed targeted mass spectrometry-based assay without retention time scheduling exemplified by Dickeya dadantii proteomic analysis during plant infection." Anal Chem; PMID: 28029036; doi: 10.1021/acs.analchem.6b03201; GPMDB: 8.
Hickox AE, Wong AC, Pak K, Strojny C, Ramirez M, Yates JR Rd, Ryan AF, Savas JN, (2016) "Global Analysis of Protein Expression of Inner Ear Hair Cells." J Neurosci; PMID: 28039372; doi: 10.1523/JNEUROSCI.2267-16.2016; GPMDB: 71.
Hansson KT, Skillbäck T, Pernevik E, Kern S, Portelius E, Höglund K, Brinkmalm G, Holmén-Larsson J, Blennow K, Zetterberg H, Gobom J, (2017) "Expanding the cerebrospinal fluid endopeptidome." Proteomics; PMID: 28044435; doi: 10.1002/pmic.201600384; GPMDB: 36.
Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR, (2017) "Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics." Cell Rep 18(1):237–247; PMID: 28052253; doi: 10.1016/j.celrep.2016.12.013; GPMDB: 128.
Cristobal A, van den Toorn HW, van de Wetering M, Clevers H, Heck AJ, Mohammed S, (2017) "Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer." Cell Rep 18(1):263–274; PMID: 28052255; doi: 10.1016/j.celrep.2016.12.016; GPMDB: 175.
Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." J Proteomics 154:102–108; PMID: 28057602; doi: 10.1016/j.jprot.2016.12.015; GPMDB: 6.
Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." Proteomics; PMID: 28058811; doi: 10.1002/pmic.201600213; GPMDB: 70.
Beck F, Geiger J, Gambaryan S, Solari FA, Dell'Aica M, Loroch S, Mattheij NJ, Mindukshev I, Pötz O, Jurk K, Burkhart JM, Fufezan C, Heemskerk JW, Walter U, Zahedi RP, Sickmann A, (2017) "Temporal quantitative phosphoproteomics of ADP stimulation reveals novel central nodes in platelet activation and inhibition." Blood 129(2):e1–e12; PMID: 28060719; doi: 10.1182/blood-2016-05-714048; GPMDB: 12.
Clotet S, Soler MJ, Riera M, Pascual J, Fang F, Zhou J, Batruch I, Vasiliou SK, Dimitromanolakis A, Barrios C, Diamandis E, Scholey J, Konvalinka A, (2017) "SILAC-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease." Mol Cell Proteomics; PMID: 28062795; doi: 10.1074/mcp.M116.061903; GPMDB: 11.
Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." Mol Cell Proteomics; PMID: 28062796; doi: 10.1074/mcp.M116.063511; GPMDB: 166.
Diaz-Vera J, Palmer S, Hernandez-Fernaud JR, Dornier E, Mitchell LE, Macpherson I, Edwards J, Zanivan S, Norman JC, (2017) "A proteomic approach to identify endosomal cargoes controlling cancer invasiveness." J Cell Sci; PMID: 28062852; doi: 10.1242/jcs.190835; GPMDB: 106.
Pietzner M, Engelmann B, Kacprowski T, Golchert J, Dirk AL, Hammer E, Iwen KA, Nauck M, Wallaschofski H, Führer D, Münte TF, Friedrich N, Völker U, Homuth G, Brabant G, (2017) "Plasma proteome and metabolome characterization of an experimental human thyrotoxicosis model." BMC Med 15(1):6; PMID: 28065164; doi: 10.1186/s12916-016-0770-8; GPMDB: 80.
Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C, (2016) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." Chemistry; PMID: 28071820; doi: 10.1002/chem.201604516; GPMDB: 6.
Xing F, Luan Y, Cai J, Wu S, Mai J, Gu J, Zhang H, Li K, Lin Y, Xiao X, Liang J, Li Y, Chen W, Tan Y, Sheng L, Lu B, Lu W, Gao M, Qiu P, Su X, Yin W, Hu J, Chen Z, Sai K, Wang J, Chen F, Chen Y, Zhu S, Liu D, Cheng S, Xie Z, Zhu W, Yan G, (2017) "The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes." Cell Rep 18(2):468–481; PMID: 28076790; doi: 10.1016/j.celrep.2016.12.037; GPMDB: 60.
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Lapek JD Jr, Lewinski MK, Wozniak JM, Guatelli J, Gonzalez DJ, (2017) "Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Vpr." Mol Cell Proteomics; PMID: 28606917; doi: 10.1074/mcp.M116.066019; GPMDB: 4.
Brocard L, Immel F, Coulon D, Esnay N, Tuphile K, Pascal S, Claverol S, Fouillen L, Bessoule JJ, Bréhélin C, (2017) "Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions." Front Plant Sci 8:894; PMID: 28611809; doi: 10.3389/fpls.2017.00894; GPMDB: 3.
Erdmann J, Junemann J, Schröder A, Just I, Gerhard R, Pich A, (2017) "Glucosyltransferase-dependent and -independent effects of TcdB on the proteome of HEp-2 cells." Proteomics; PMID: 28612519; doi: 10.1002/pmic.201600435; GPMDB: 36.
Murgia M, Toniolo L, Nagaraj N, Ciciliot S, Vindigni V, Schiaffino S, Reggiani C, Mann M, (2017) "Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging." Cell Rep 19(11):2396–2409; PMID: 28614723; doi: 10.1016/j.celrep.2017.05.054; GPMDB: 174.
Plenker D, Riedel M, Brägelmann J, Dammert MA, Chauhan R, Knowles PP, Lorenz C, Keul M, Bührmann M, Pagel O, Tischler V, Scheel AH, Schütte D, Song Y, Stark J, Mrugalla F, Alber Y, Richters A, Engel J, Leenders F, Heuckmann JM, Wolf J, Diebold J, Pall G, Peifer M, Aerts M, Gevaert K, Zahedi RP, Buettner R, Shokat KM, McDonald NQ, Kast SM, Gautschi O, Thomas RK, Sos ML, (2017) "Drugging the catalytically inactive state of RET kinase in RET-rearranged tumors." Sci Transl Med 9(394):; PMID: 28615362; doi: 10.1126/scitranslmed.aah6144; GPMDB: 17.
Marx H, Hahne H, Ulbrich SE, Schnieke A, Rottmann O, Frishman D, Kuster B, (2017) "Annotation of the Domestic Pig Genome by Quantitative Proteogenomics." J Proteome Res; PMID: 28625053; doi: 10.1021/acs.jproteome.7b00184; GPMDB: 181.
Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM, (2017) "Colorectal Cancer Cell Line Proteomes are Representative of Primary Tumors and Predict Drug Sensitivity." Gastroenterology; PMID: 28625833; doi: 10.1053/j.gastro.2017.06.008; GPMDB: 44.
Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T, (2017) "Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma." Proteomics Clin Appl; PMID: 28626882; doi: 10.1002/prca.201700014; GPMDB: 56.
Qin G, Dang M, Gao H, Wang H, Luo F, Chen R, (2017) "Deciphering the protein-protein interaction network regulating hepatocellular carcinoma metastasis." Biochim Biophys Acta 1865(9):1114–1122; PMID: 28627476; doi: 10.1016/j.bbapap.2017.06.005; GPMDB: 6.
Sung E, Kwon OK, Lee JM, Lee S, (2017) "Proteomics approach to identify novel metastatic bone markers from the secretome of PC-3 prostate cancer cells." Electrophoresis; PMID: 28627741; doi: 10.1002/elps.201700052; GPMDB: 2.
Loke I, Østergaard O, Heegaard NHH, Packer NH, Thaysen-Andersen M, (2017) "Paucimannose-Rich N-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions." Mol Cell Proteomics; PMID: 28630087; doi: 10.1074/mcp.M116.066746; GPMDB: 118.
Ahsan N, Belmont J, Chen Z, Clifton JG, Salomon AR, (2017) "Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction." J Proteomics 165:69–74; PMID: 28634120; doi: 10.1016/j.jprot.2017.06.013; GPMDB: 30.
Feil G, Horres R, Schulte J, Mack AF, Petzoldt S, Arnold C, Meng C, Jost L, Boxleitner J, Kiessling-Wolf N, Serbest E, Helm D, Kuster B, Hartmann I, Korff T, Hahne H, (2017) "Bacterial cellulose shifts transcriptome and proteome of cultured endothelial cells towards native differentiation." Mol Cell Proteomics; PMID: 28637836; doi: 10.1074/mcp.RA117.000001; GPMDB: 2.
Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO, (2017) "Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice." J Proteome Res; PMID: 28641008; doi: 10.1021/acs.jproteome.7b00144; GPMDB: 39.
Belmont J, Gu T, Mudd A, Salomon AR, (2017) "A PLC-γ1 Feedback Pathway Regulates Lck Substrate Phosphorylation at the T-Cell Receptor and SLP-76 Complex." J Proteome Res; PMID: 28644030; doi: 10.1021/acs.jproteome.6b01026; GPMDB: 60.
Henriet E, Abou Hammoud A, Dupuy JW, Dartigues B, Ezzoukry Z, Dugot-Senant N, Leste-Lasserre T, Pallares-Lupon N, Nikolski M, Le Bail B, Blanc JF, Balabaud C, Bioulac-Sage P, Raymond AA, Saltel F, (2017) "Argininosuccinate synthase 1 (ASS1): A marker of unclassified hepatocellular adenoma and high bleeding risk." Hepatology 66(6):2016–2028; PMID: 28646562; doi: 10.1002/hep.29336; GPMDB: 124.
Gu Y, Albuquerque CP, Braas D, Zhang W, Villa GR, Bi J, Ikegami S, Masui K, Gini B, Yang H, Gahman TC, Shiau AK, Cloughesy TF, Christofk HR, Zhou H, Guan KL, Mischel PS, (2017) "mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT." Mol Cell 67(1):128–138.e7; PMID: 28648777; doi: 10.1016/j.molcel.2017.05.030; GPMDB: 2.
Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M, (2017) "The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1." Mol Cell 67(2):294–307.e9; PMID: 28648780; doi: 10.1016/j.molcel.2017.05.026; GPMDB: 50.
Morgenstern M, Stiller SB, Lübbert P, Peikert CD, Dannenmaier S, Drepper F, Weill U, Höß P, Feuerstein R, Gebert M, Bohnert M, van der Laan M, Schuldiner M, Schütze C, Oeljeklaus S, Pfanner N, Wiedemann N, Warscheid B, (2017) "Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale." Cell Rep 19(13):2836–2852; PMID: 28658629; doi: 10.1016/j.celrep.2017.06.014; GPMDB: 697.
Offenburger SL, Bensaddek D, Murillo AB, Lamond AI, Gartner A, (2017) "Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development." Sci Rep 7(1):4314; PMID: 28659600; doi: 10.1038/s41598-017-04375-4; GPMDB: 289.
Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D, (2017) "Comparison of fractionation proteomics for local SWATH library building." Proteomics; PMID: 28664598; doi: 10.1002/pmic.201700052; GPMDB: 4.
Sap KA, Bezstarosti K, Dekkers DHW, Voets O, Demmers JAA, (2017) "Quantitative Proteomics Reveals Extensive Changes in the Ubiquitinome after Perturbation of the Proteasome by Targeted dsRNA-Mediated Subunit Knockdown in Drosophila." J Proteome Res; PMID: 28665616; doi: 10.1021/acs.jproteome.7b00156; GPMDB: 290.
Hulme CH, Wilson EL, Peffers MJ, Roberts S, Simpson DM, Richardson JB, Gallacher P, Wright KT, (2017) "Autologous chondrocyte implantation-derived synovial fluids display distinct responder and non-responder proteomic profiles." Arthritis Res Ther 19(1):150; PMID: 28666451; doi: 10.1186/s13075-017-1336-7; GPMDB: 37.
Yu Y, Bekele S, Pieper R, (2017) "Quick 96FASP for high throughput quantitative proteome analysis." J Proteomics 166:1–7; PMID: 28669814; doi: 10.1016/j.jprot.2017.06.019; GPMDB: 15.
Kim JH, Nam WS, Kim SJ, Kwon OK, Seung EJ, Jo JJ, Shresha R, Lee TH, Jeon TW, Ki SH, Lee HS, Lee S, (2017) "Mechanism Investigation of Rifampicin-Induced Liver Injury Using Comparative Toxicoproteomics in Mice." Int J Mol Sci 18(7):; PMID: 28671602; doi: 10.3390/ijms18071417; GPMDB: 10.
Liu F, Meng H, Fitzgerald MC, (2017) "Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using SILAC-SPROX." J Proteome Res; PMID: 28673085; doi: 10.1021/acs.jproteome.7b00283; GPMDB: 6.
Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F, (2017) "MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress." Proc Natl Acad Sci U S A 114(29):7671–7676; PMID: 28673974; doi: 10.1073/pnas.1620208114; GPMDB: 6.
Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J, (2017) "Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome." Sci Rep 7(1):4513; PMID: 28674419; doi: 10.1038/s41598-017-04798-z; GPMDB: 133.
Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS, (2017) "Genes essential for phototrophic growth by a purple alphaproteobacterium." Environ Microbiol; PMID: 28677146; doi: 10.1111/1462-2920.13852; GPMDB: 6.
Soman KV, Stafford SJ, Pazdrak K, Wu Z, Luo X, White WI, Wiktorowicz JE, Calhoun WJ, Kurosky A, (2017) "Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study." J Proteome Res 16(8):2663–2679; PMID: 28679203; doi: 10.1021/acs.jproteome.6b00367; GPMDB: 47.
Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM, (2017) "HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma." Cancer Metab 5:5; PMID: 28680592; doi: 10.1186/s40170-017-0167-y; GPMDB: 12.
Zwittink RD, van Zoeren-Grobben D, Martin R, van Lingen RA, Groot Jebbink LJ, Boeren S, Renes IB, van Elburg RM, Belzer C, Knol J, (2017) "Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants." Mol Cell Proteomics; PMID: 28684633; doi: 10.1074/mcp.RA117.000102; GPMDB: 65.
Djuric U, Rodrigues DC, Batruch I, Ellis J, Shannon P, Diamandis P, (2017) "Spatiotemporal proteomic profiling of human cerebral development." Mol Cell Proteomics; PMID: 28687556; doi: 10.1074/mcp.M116.066274; GPMDB: 99.
Bryk AH, Wiśniewski JR, (2017) "Quantitative Analysis of Human Red Blood Cell Proteome." J Proteome Res 16(8):2752–2761; PMID: 28689405; doi: 10.1021/acs.jproteome.7b00025; GPMDB: 96.
Reid SE, Kay EJ, Neilson LJ, Henze AT, Serneels J, McGhee EJ, Dhayade S, Nixon C, Mackey JB, Santi A, Swaminathan K, Athineos D, Papalazarou V, Patella F, Román-Fernández Á, ElMaghloob Y, Hernandez-Fernaud JR, Adams RH, Ismail S, Bryant DM, Salmeron-Sanchez M, Machesky LM, Carlin LM, Blyth K, Mazzone M, Zanivan S, (2017) "Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium." EMBO J; PMID: 28694244; doi: 10.15252/embj.201694912; GPMDB: 19.
Ovelleiro D, Blanco S, Hernández R, Peinado MÁ, (2017) "Comparative proteomic study of early hypoxic response in the cerebral cortex of rats submitted to two different hypoxic models." Proteomics Clin Appl; PMID: 28697276; doi: 10.1002/prca.201700058; GPMDB: 19.
Zhang X, Li L, Mayne J, Ning Z, Stintzi A, Figeys D, (2017) "Assessing the impact of protein extraction methods for human gut metaproteomics." J Proteomics; PMID: 28705725; doi: 10.1016/j.jprot.2017.07.001; GPMDB: 30.
Kohli P, Höhne M, Jüngst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B, (2017) "The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia." EMBO Rep; PMID: 28710093; doi: 10.15252/embr.201643846; GPMDB: 20.
Hongliang L, Lei Z, Qing W, Zhaopeng S, Xiaoyan S, Juan D, Chenyang H, Yong Z, Zekun G, (2017) "Comprehensive Proteomic Analysis of PGC7-Interacting Proteins." J Proteome Res; PMID: 28712289; doi: 10.1021/acs.jproteome.6b00883; GPMDB: 10.
Chai H, Diaz-Castro B, Shigetomi E, Monte E, Octeau JC, Yu X, Cohn W, Rajendran PS, Vondriska TM, Whitelegge JP, Coppola G, Khakh BS, (2017) "Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence." Neuron 95(3):531–549.e9; PMID: 28712653; doi: 10.1016/j.neuron.2017.06.029; GPMDB: 4.
Vukotic M, Nolte H, König T, Saita S, Ananjew M, Krüger M, Tatsuta T, Langer T, (2017) "Acylglycerol Kinase Mutated in Sengers Syndrome Is a Subunit of the TIM22 Protein Translocase in Mitochondria." Mol Cell 67(3):471–483.e7; PMID: 28712724; doi: 10.1016/j.molcel.2017.06.013; GPMDB: 59.
Alfieri A, Sorokina O, Adrait A, Angelini C, Russo I, Morellato A, Matteoli M, Menna E, Boeri Erba E, McLean C, Armstrong JD, Ala U, Buxbaum JD, Brusco A, Couté Y, De Rubeis S, Turco E, Defilippi P, (2017) "Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders." Front Mol Neurosci 10:212; PMID: 28713243; doi: 10.3389/fnmol.2017.00212; GPMDB: 12.
Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S, (2017) "Outer Membrane Proteome of Veillonella parvula: A Diderm Firmicute of the Human Microbiome." Front Microbiol 8:1215; PMID: 28713344; doi: 10.3389/fmicb.2017.01215; GPMDB: 16.
Lee HJ, Jedrychowski MP, Vinayagam A, Wu N, Shyh-Chang N, Hu Y, Min-Wen C, Moore JK, Asara JM, Lyssiotis CA, Perrimon N, Gygi SP, Cantley LC, Kirschner MW, (2017) "Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation." Cell Rep 20(3):721–736; PMID: 28723573; doi: 10.1016/j.celrep.2017.06.074; GPMDB: 2.
La Barbera G, Capriotti AL, Michelini E, Piovesana S, Calabretta MM, Chiozzi RZ, Roda A, Laganà A, (2017) "Proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells." Proteomics; PMID: 28727291; doi: 10.1002/pmic.201700081; GPMDB: 13.
Mir SA, Renuse S, Sathe G, Khan AA, Patil AH, Nanjappa V, Bhat FA, Prasad TSK, Giri AK, Chatterjee A, Gowda H, (2017) "Altered signaling associated with chronic arsenic exposure in human skin keratinocytes." Proteomics Clin Appl; PMID: 28731282; doi: 10.1002/prca.201700004; GPMDB: 2.
Maffioli E, Nonnis S, Angioni R, Santagata F, Calì B, Zanotti L, Negri A, Viola A, Tedeschi G, (2017) "Proteomic analysis of the secretome of human bone marrow-derived mesenchymal stem cells primed by pro-inflammatory cytokines." J Proteomics 166:115–126; PMID: 28739509; doi: 10.1016/j.jprot.2017.07.012; GPMDB: 20.
Hau AC, Grebbin BM, Agoston Z, Anders-Maurer M, Müller T, Groß A, Kolb J, Langer JD, Döring C, Schulte D, (2017) "MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1." J Cell Biol; PMID: 28739678; doi: 10.1083/jcb.201701154; GPMDB: 6.
Girardi T, Vereecke S, Sulima SO, Khan Y, Fancello L, Briggs JW, Schwab C, de Beeck JO, Verbeeck J, Royaert J, Geerdens E, Vicente C, Bornschein S, Harrison CJ, Meijerink JP, Cools J, Dinman JD, Kampen KR, De Keersmaecker K, (2017) "The T-cell leukemia-associated ribosomal RPL10 R98S mutation enhances JAK-STAT signaling." Leukemia; PMID: 28744013; doi: 10.1038/leu.2017.225; GPMDB: 36.
D'Angelo G, Chaerkady R, Yu W, Hizal DB, Hess S, Zhao W, Lekstrom K, Guo X, White WI, Roskos L, Bowen MA, Yang H, (2017) "Statistical models for the analysis of isobaric tags multiplexed quantitative proteomics." J Proteome Res; PMID: 28745510; doi: 10.1021/acs.jproteome.6b01050; GPMDB: 5.
Komor MA, Pham T, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA, (2017) "Identification of differentially expressed splice variants by the proteogenomic pipeline Splicify." Mol Cell Proteomics; PMID: 28747380; doi: 10.1074/mcp.TIR117.000056; GPMDB: 14.
Zhang X, Chen W, Ning Z, Mayne J, Mack D, Stintzi A, Tian R, Figeys D, (2017) "Deep Metaproteomics Approach for the Study of Human Microbiomes." Anal Chem; PMID: 28749657; doi: 10.1021/acs.analchem.7b02224; GPMDB: 43.
Haderk F, Schulz R, Iskar M, Cid LL, Worst T, Willmund KV, Schulz A, Warnken U, Seiler J, Benner A, Nessling M, Zenz T, Göbel M, Dürig J, Diederichs S, Paggetti J, Moussay E, Stilgenbauer S, Zapatka M, Lichter P, Seiffert M, (2017) "Tumor-derived exosomes modulate PD-L1 expression in monocytes." Sci Immunol 2(13):; PMID: 28754746; doi: 10.1126/sciimmunol.aah5509; GPMDB: 32.
Singh KD, Zheng X, Milstein S, Keller M, Roschitzki B, Grossmann J, Hengartner MO, (2017) "Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans." PLoS One 12(7):e0182270; PMID: 28759574; doi: 10.1371/journal.pone.0182270; GPMDB: 6.
Gómez-Baena G, Bennett RJ, Martínez-Rodríguez C, Wnęk M, Laing G, Hickey G, McLean L, Beynon RJ, Carrol ED, (2017) "Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis." Sci Rep 7(1):7042; PMID: 28765563; doi: 10.1038/s41598-017-07127-6; GPMDB: 28.
Wegler C, Gaugaz FZ, Andersson TB, Wiśniewski JR, Busch D, Gröer C, Oswald S, Norén A, Weiss F, Hammer HS, Joos TO, Poetz O, Achour B, Rostami-Hodjegan A, van de Steeg E, Wortelboer HM, Artursson P, (2017) "Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes." Mol Pharm 14(9):3142–3151; PMID: 28767254; doi: 10.1021/acs.molpharmaceut.7b00364; GPMDB: 6.
Fabiani FD, Renault TT, Peters B, Dietsche T, Gálvez EJC, Guse A, Freier K, Charpentier E, Strowig T, Franz-Wachtel M, Macek B, Wagner S, Hensel M, Erhardt M, (2017) "A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum." PLoS Biol 15(8):e2002267; PMID: 28771474; doi: 10.1371/journal.pbio.2002267; GPMDB: 26.
Nguyen AT, Prado MA, Schmidt PJ, Sendamarai AK, Wilson-Grady JT, Min M, Campagna DR, Tian G, Shi Y, Dederer V, Kawan M, Kuehnle N, Paulo JA, Yao Y, Weiss MJ, Justice MJ, Gygi SP, Fleming MD, Finley D, (2017) "UBE2O remodels the proteome during terminal erythroid differentiation." Science 357(6350):; PMID: 28774900; doi: 10.1126/science.aan0218; GPMDB: 13.
Khan MH, Salomaa SI, Jacquemet G, Butt U, Miihkinen M, Deguchi T, Kremneva E, Lappalainen P, Humphries MJ, Pouwels J, (2017) "The Sharpin interactome reveals a role for Sharpin in lamellipodium formation via the Arp2/3 complex." J Cell Sci; PMID: 28775156; doi: 10.1242/jcs.200329; GPMDB: 51.
Woo J, Han D, Wang JI, Park J, Kim H, Kim Y, (2017) "Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation." J Proteome Res 16(9):3419–3432; PMID: 28777000; doi: 10.1021/acs.jproteome.7b00445; GPMDB: 18.
Danielsen HN, Hansen SH, Herbst FA, Kjeldal H, Stensballe A, Nielsen PH, Dueholm MS, (2017) "Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry." Biomolecules 7(3):; PMID: 28777328; doi: 10.3390/biom7030058; GPMDB: 24.
Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyö D, Held JM, (2017) "Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner." Sci Signal 10(491):; PMID: 28790197; doi: 10.1126/scisignal.aam8065; GPMDB: 10.
Dong M, Bian Y, Wang Y, Dong J, Yao Y, Deng Z, Qin H, Zou H, Ye M, (2017) "Sensitive, Robust, and Cost-Effective Approach for Tyrosine Phosphoproteome Analysis." Anal Chem 89(17):9307–9314; PMID: 28796482; doi: 10.1021/acs.analchem.7b02078; GPMDB: 24.
Anselm V, Novikova S, Zgoda V, (2017) "Re-adaption on Earth after Spaceflights Affects the Mouse Liver Proteome." Int J Mol Sci 18(8):; PMID: 28805685; doi: 10.3390/ijms18081763; GPMDB: 28.
Barbé C, Bray F, Gueugneau M, Devassine S, Lause P, Tokarski C, Rolando C, Thissen JP, (2017) "Comparative Proteomic and Transcriptomic Analysis of Follistatin-Induced Skeletal Muscle Hypertrophy." J Proteome Res; PMID: 28810121; doi: 10.1021/acs.jproteome.7b00069; GPMDB: 72.
Cortes T, Schubert OT, Banaei-Esfahani A, Collins BC, Aebersold R, Young DB, (2017) "Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival." Sci Rep 7(1):8208; PMID: 28811595; doi: 10.1038/s41598-017-08306-1; GPMDB: 30.
Pardo M, Yu L, Shen S, Tate P, Bode D, Letney BL, Quelle DE, Skarnes W, Choudhary JS, (2017) "Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells." Sci Rep 7(1):8157; PMID: 28811661; doi: 10.1038/s41598-017-08456-2; GPMDB: 236.
Park J, Han D, Do M, Woo J, Wang JI, Han Y, Kwon W, Kim SW, Jang JY, Kim Y, (2017) "Proteome Characterization of Human Pancreatic Cyst Fluid from Intraductal Papillary Mucinous Neoplasm by LC/MS/MS." Rapid Commun Mass Spectrom; PMID: 28815810; doi: 10.1002/rcm.7959; GPMDB: 60.
Dammalli M, Dey G, Madugundu AK, Kumar M, Rodrigues B, Gowda H, Siddaiah BG, Mahadevan A, Shankar SK, Prasad TSK, (2017) "Proteomic Analysis of the Human Olfactory Bulb." OMICS 21(8):440–453; PMID: 28816642; doi: 10.1089/omi.2017.0084; GPMDB: 2.
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Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." Sci Rep 7(1):8642; PMID: 28819186; doi: 10.1038/s41598-017-08094-8; GPMDB: 146.
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Phillips TJ, Scott H, Menassa DA, Bignell AL, Sood A, Morton JS, Akagi T, Azuma K, Rogers MF, Gilmore CE, Inman GJ, Grant S, Chung Y, Aljunaidy MM, Cooke CL, Steinkraus BR, Pocklington A, Logan A, Collett GP, Kemp H, Holmans PA, Murphy MP, Fulga TA, Coney AM, Akashi M, Davidge ST, Case CP, (2017) "Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development." Sci Rep 7(1):9079; PMID: 28831049; doi: 10.1038/s41598-017-06300-1; GPMDB: 1.
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Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL, (2017) "Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain." Sci Rep 7(1):9520; PMID: 28842697; doi: 10.1038/s41598-017-10422-x; GPMDB: 22.
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Guo J, Wang P, Cheng Q, Sun L, Wang H, Wang Y, Kao L, Li Y, Qiu T, Yang W, Shen H, (2017) "Proteomic analysis reveals strong mitochondrial involvement in cytoplasmic male sterility of pepper (Capsicum annuum L.)." J Proteomics 168:15–27; PMID: 28847649; doi: 10.1016/j.jprot.2017.08.013; GPMDB: 6.
Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." Mol Cell Proteomics; PMID: 28851738; doi: 10.1074/mcp.M117.067355; GPMDB: 6.
Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, (2017) "Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague." PLoS One 12(8):e0183478; PMID: 28854255; doi: 10.1371/journal.pone.0183478; GPMDB: 343.
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Subramanian K, Rauniyar N, Lavalleé-Adam M, Yates JR 3rd, Balch WE, (2017) "Quantitative Analysis of the Proteome Response to the Histone Deacetylase Inhibitor (HDACi) Vorinostat in Niemann-Pick Type C1 disease." Mol Cell Proteomics; PMID: 28860124; doi: 10.1074/mcp.M116.064949; GPMDB: 7.
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Tanabe Y, Naito Y, Vasuta C, Lee AK, Soumounou Y, Linhoff MW, Takahashi H, (2017) "IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α." Nat Commun 8(1):408; PMID: 28864826; doi: 10.1038/s41467-017-00333-w; GPMDB: 32.
Kraner ME, Müller C, Sonnewald U, (2017) "Comparative proteomic profiling of the Choline transporter-like1 (CHER1) mutant provides insights into plasmodesmata composition of fully developed Arabidopsis thaliana leaves." Plant J; PMID: 28865150; doi: 10.1111/tpj.13702; GPMDB: 1.
Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, Wang SY, Baltissen MPA, Jansen PWTC, Rossa M, Müller M, Stunnenberg HG, He C, Carell T, Vermeulen M, (2017) "N⁶-methyladenosine (m⁶A) recruits and repels proteins to regulate mRNA homeostasis." Nat Struct Mol Biol; PMID: 28869609; doi: 10.1038/nsmb.3462; GPMDB: 40.
Liu MQ, Zeng WF, Fang P, Cao WQ, Liu C, Yan GQ, Zhang Y, Peng C, Wu JQ, Zhang XJ, Tu HJ, Chi H, Sun RX, Cao Y, Dong MQ, Jiang BY, Huang JM, Shen HL, Wong CCL, He SM, Yang PY, (2017) "pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification." Nat Commun 8(1):438; PMID: 28874712; doi: 10.1038/s41467-017-00535-2; GPMDB: 4.
Dittus L, Werner T, Muelbaier M, Bantscheff M, (2017) "Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors." ACS Chem Biol 12(10):2515–2521; PMID: 28876896; doi: 10.1021/acschembio.7b00617; GPMDB: 154.
Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Rohner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Dietzen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weigmann B, Ziegler AG, Mann M, Tschöp MH, Daniel C, (2017) "A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function." Cell Metab 26(3):475–492.e7; PMID: 28877454; doi: 10.1016/j.cmet.2017.08.008; GPMDB: 31.
Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS, (2017) "APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism." Nat Commun 8(1):465; PMID: 28878238; doi: 10.1038/s41467-017-00493-9; GPMDB: 18.
Han B, Fang Y, Feng M, Hu H, Hao Y, Ma C, Huo X, Meng L, Zhang X, Wu F, Li J, (2017) "Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers." J Proteome Res; PMID: 28879772; doi: 10.1021/acs.jproteome.7b00371; GPMDB: 47.
Phillips B, Titz B, Kogel U, Sharma D, Leroy P, Xiang Y, Vuillaume G, Lebrun S, Sciuscio D, Ho J, Nury C, Guedj E, Elamin A, Esposito M, Krishnan S, Schlage WK, Veljkovic E, Ivanov NV, Martin F, Peitsch MC, Hoeng J, Vanscheeuwijck P, (2017) "Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints." Food Chem Toxicol 109(Pt 1):315–332; PMID: 28882640; doi: 10.1016/j.fct.2017.09.001; GPMDB: 36.
Pawellek A, Ryder U, Tammsalu T, King LJ, Kreinin H, Ly T, Hay RT, Hartley RC, Lamond AI, (2017) "Characterisation of the biflavonoid hinokiflavone as a pre-mRNA splicing modulator that inhibits SENP." Elife; PMID: 28884683; doi: 10.7554/eLife.27402; GPMDB: 6.
Kishazi E, Dor M, Eperon S, Oberic A, Hamedani M, Turck N, (2017) "Thyroid-associated orbitopathy and tears: A proteomics study." J Proteomics; PMID: 28887209; doi: 10.1016/j.jprot.2017.09.001; GPMDB: 8.
Rijkers M, van den Eshof BL, van der Meer PF, van Alphen FPJ, de Korte D, Leebeek FWG, Meijer AB, Voorberg J, Jansen AJG, (2017) "Monitoring storage induced changes in the platelet proteome employing label free quantitative mass spectrometry." Sci Rep 7(1):11045; PMID: 28887518; doi: 10.1038/s41598-017-11643-w; GPMDB: 21.
Bachofner M, Speicher T, Bogorad RL, Muzumdar S, Derrer CP, Hürlimann F, Böhm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altés S, Graf R, Anderson DG, Koteliansky V, Auf dem Keller U, Werner S, (2017) "Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration." Dev Cell; PMID: 28890072; doi: 10.1016/j.devcel.2017.07.025; GPMDB: 20.
Lapek JD Jr, Greninger P, Morris R, Amzallag A, Pruteanu-Malinici I, Benes CH, Haas W, (2017) "Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities." Nat Biotechnol; PMID: 28892078; doi: 10.1038/nbt.3955; GPMDB: 11.
McNally KE, Faulkner R, Steinberg F, Gallon M, Ghai R, Pim D, Langton P, Pearson N, Danson CM, Nägele H, Morris LL, Singla A, Overlee BL, Heesom KJ, Sessions R, Banks L, Collins BM, Berger I, Billadeau DD, Burstein E, Cullen PJ, (2017) "Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling." Nat Cell Biol 19(10):1214–1225; PMID: 28892079; doi: 10.1038/ncb3610; GPMDB: 23.
Guccione EJ, Kendall JJ, Hitchcock A, Garg N, White MA, Mulholland F, Poole RK, Kelly DJ, (2017) "Transcriptome and proteome dynamics in chemostat culture reveal how Campylobacter jejuni modulates metabolism, stress responses and virulence factors upon changes in oxygen availability." Environ Microbiol; PMID: 28892295; doi: 10.1111/1462-2920.13930; GPMDB: 54.
Bardot P, Vincent SD, Fournier M, Hubaud A, Joint M, Tora L, Pourquié O, (2017) "The TAF10-containing TFIID and SAGA transcriptional complexes are dispensable for early somitogenesis in the mouse embryo." Development; PMID: 28893950; doi: 10.1242/dev.146902; GPMDB: 30.
Avenarius MR, Krey JF, Dumont RA, Morgan CP, Benson CB, Vijayakumar S, Cunningham CL, Scheffer DI, Corey DP, Müller U, Jones SM, Barr-Gillespie PG, (2017) "Heterodimeric capping protein is required for stereocilia length and width regulation." J Cell Biol; PMID: 28899994; doi: 10.1083/jcb.201704171; GPMDB: 52.
Rowland EA, Greco TM, Snowden CK, McCabe AL, Silhavy TJ, Cristea IM, (2017) "Sirtuin Lipoamidase Activity Is Conserved in Bacteria as a Regulator of Metabolic Enzyme Complexes." MBio 8(5):; PMID: 28900027; doi: 10.1128/mBio.01096-17; GPMDB: 2.
Midgett M, López CS, David L, Maloyan A, Rugonyi S, (2017) "Increased Hemodynamic Load in Early Embryonic Stages Alters Myofibril and Mitochondrial Organization in the Myocardium." Front Physiol 8:631; PMID: 28912723; doi: 10.3389/fphys.2017.00631; GPMDB: 1.
Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." Leukemia; PMID: 28914261; doi: 10.1038/leu.2017.284; GPMDB: 17.
Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." Mol Syst Biol 13(9):939; PMID: 28916541; GPMDB: 92.
Mills RJ, Titmarsh DM, Koenig X, Parker BL, Ryall JG, Quaife-Ryan GA, Voges HK, Hodson MP, Ferguson C, Drowley L, Plowright AT, Needham EJ, Wang QD, Gregorevic P, Xin M, Thomas WG, Parton RG, Nielsen LK, Launikonis BS, James DE, Elliott DA, Porrello ER, Hudson JE, (2017) "Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest." Proc Natl Acad Sci U S A 114(40):E8372–E8381; PMID: 28916735; doi: 10.1073/pnas.1707316114; GPMDB: 8.
Martin-Perez M, Villén J, (2017) "Determinants and Regulation of Protein Turnover in Yeast." Cell Syst 5(3):283–294.e5; PMID: 28918244; doi: 10.1016/j.cels.2017.08.008; GPMDB: 12.
Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." Cell Chem Biol; PMID: 28919039; doi: 10.1016/j.chembiol.2017.08.006; GPMDB: 16.
Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, (2017) "Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection." Nat Microbiol; PMID: 28924191; doi: 10.1038/s41564-017-0021-6; GPMDB: 15.
Liao Y, Weber D, Xu W, Durbin-Johnson BP, Phinney BS, Lönnerdal B, (2017) "Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation." J Proteome Res 16(11):4113–4121; PMID: 28925267; doi: 10.1021/acs.jproteome.7b00486; GPMDB: 93.
Lum KM, Sato Y, Beyer BA, Plaisted WC, Anglin JL, Lairson LL, Cravatt BF, (2017) "Mapping Protein Targets of Bioactive Small Molecules Using Lipid-Based Chemical Proteomics." ACS Chem Biol; PMID: 28930429; doi: 10.1021/acschembio.7b00581; GPMDB: 43.
Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ, (2017) "Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins." Elife; PMID: 28933694; doi: 10.7554/eLife.26435; GPMDB: 4.
Mackinder LCM, Chen C, Leib RD, Patena W, Blum SR, Rodman M, Ramundo S, Adams CM, Jonikas MC, (2017) "A Spatial Interactome Reveals the Protein Organization of the Algal CO₂-Concentrating Mechanism." Cell 171(1):133–147.e14; PMID: 28938113; doi: 10.1016/j.cell.2017.08.044; GPMDB: 168.
Velásquez E, Nogueira FCS, Velásquez I, Schmitt A, Falkai P, Domont GB, Martins de Souza D, (2017) "Synaptosomal proteome of the orbitofrontal cortex from schizophrenia patients using quantitative label-free and iTRAQ-based shotgun proteomics." J Proteome Res; PMID: 28949146; doi: 10.1021/acs.jproteome.7b00422; GPMDB: 3.
Cuijpers SAG, Willemstein E, Vertegaal ACO, (2017) "Converging SUMO and ubiquitin signaling: improved methodology identifies co-modified target proteins." Mol Cell Proteomics; PMID: 28951443; doi: 10.1074/mcp.TIR117.000152; GPMDB: 102.
Seddigh P, Bracht T, Molinier-Frenkel V, Castellano F, Kniemeyer O, Schuster M, Weski J, Hasenberg A, Kraus A, Poschet G, Hager T, Theegarte D, Opitz C, Brakhage AA, Sitek B, Hasenberg M, Gunzer M, (2017) "Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary Aspergillus fumigatus Infection." Mol Cell Proteomics; PMID: 28951444; doi: 10.1074/mcp.RA117.000072; GPMDB: 18.
Wang Q, Lu Q, (2017) "Plasma membrane-derived extracellular microvesicles mediate non-canonical intercellular NOTCH signaling." Nat Commun 8(1):709; PMID: 28955033; doi: 10.1038/s41467-017-00767-2; GPMDB: 2.
Triana S, de Cock H, Ohm RA, Danies G, Wösten HAB, Restrepo S, González Barrios AF, Celis A, (2017) "Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling." Front Microbiol 8:1772; PMID: 28959251; doi: 10.3389/fmicb.2017.01772; GPMDB: 37.
Megger DA, Philipp J, Le-Trilling VTK, Sitek B, Trilling M, (2017) "Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression." Front Immunol 8:1139; PMID: 28959263; doi: 10.3389/fimmu.2017.01139; GPMDB: 114.
Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P, (2017) "Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue." J Proteome Res; PMID: 28959888; doi: 10.1021/acs.jproteome.7b00340; GPMDB: 63.
Stadlmann J, Taubenschmid J, Wenzel D, Gattinger A, Dürnberger G, Dusberger F, Elling U, Mach L, Mechtler K, Penninger JM, (2017) "Comparative glycoproteomics of stem cells identifies new players in ricin toxicity." Nature 549(7673):538–542; PMID: 28959962; doi: 10.1038/nature24015; GPMDB: 1.
Li S, He Y, Lin Z, Xu S, Zhou R, Liang F, Wang J, Yang H, Liu S, Ren Y, (2017) "Digging more missing proteins using an enrichment approach with ProteoMiner™." J Proteome Res; PMID: 28960076; doi: 10.1021/acs.jproteome.7b00353; GPMDB: 199.
Hauser DN, Mamais A, Conti MM, Primiani CT, Kumaran R, Dillman AA, Langston RG, Beilina A, Garcia JH, Diaz-Ruiz A, Bernier M, Fiesel FC, Hou X, Springer W, Li Y, de Cabo R, Cookson MR, (2017) "Hexokinases link DJ-1 to the PINK1/parkin pathway." Mol Neurodegener 12(1):70; PMID: 28962651; doi: 10.1186/s13024-017-0212-x; GPMDB: 6.
Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T, (2017) "Detergent-insoluble proteome analysis revealed aberrantly aggregated proteins in human preeclampsia placentas." J Proteome Res; PMID: 28965414; doi: 10.1021/acs.jproteome.7b00352; GPMDB: 4.
Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD, (2017) "Identifying host factors associated with DNA replicated during virus infection." Mol Cell Proteomics; PMID: 28972080; doi: 10.1074/mcp.M117.067116; GPMDB: 164.
Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA, (2017) "Systems-level identification of PKA-dependent signaling in epithelial cells." Proc Natl Acad Sci U S A 114(42):E8875–E8884; PMID: 28973931; doi: 10.1073/pnas.1709123114; GPMDB: 75.
Bjørkum AA, Oveland E, Stuhr L, Havnes MB, Berven F, Grønning M, Hope A, (2017) "Fast hyperbaric decompression after heliox saturation altered the brain proteome in rats." PLoS One 12(10):e0185765; PMID: 28977037; doi: 10.1371/journal.pone.0185765; GPMDB: 19.
Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." Oncotarget 8(40):68493–68516; PMID: 28978133; doi: 10.18632/oncotarget.19663; GPMDB: 23.
Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." Mol Cell Proteomics; PMID: 28982715; doi: 10.1074/mcp.M116.066654; GPMDB: 268.
Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski J, Richter EA, James DE, (2017) "Multiplexed temporal quantification of the exercise-regulated plasma peptidome." Mol Cell Proteomics; PMID: 28982716; doi: 10.1074/mcp.RA117.000020; GPMDB: 12.
Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Carson D, Pevsner-Fischer M, Furniss RCD, Dougan G, Dori-Bachash M, Yu L, Clements A, Collins JW, Elinav E, Larrouy-Maumus GJ, Choudhary JS, Frankel G, (2017) "Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo." Cell Metab 26(5):738–752.e6; PMID: 28988824; doi: 10.1016/j.cmet.2017.09.003; GPMDB: 24.
Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U, (2017) "Polypharmacology-based ceritinib repurposing using integrated functional proteomics." Nat Chem Biol 13(12):1222–1231; PMID: 28991240; doi: 10.1038/nchembio.2489; GPMDB: 73.
Novikova SE, Tikhonova OV, Kurbatov LK, Farafonova TE, Vakhrushev IV, Zgoda VG, (2017) "Application of selected reaction monitoring and parallel reaction monitoring for investigation of HL-60 cell line differentiation." Eur J Mass Spectrom (Chichester) 23(4):202–208; PMID: 29028392; doi: 10.1177/1469066717719848; GPMDB: 25.
Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." Sci Rep 7(1):13136; PMID: 29030565; doi: 10.1038/s41598-017-13197-3; GPMDB: 43.
Grenga L, Chandra G, Saalbach G, Galmozzi CV, Kramer G, Malone JG, (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." Front Microbiol 8:1784; PMID: 29033902; doi: 10.3389/fmicb.2017.01784; GPMDB: 1.
Kugeratski FG, Batista M, Lima CVP, Neilson LJ, da Cunha ES, de Godoy LMF, Zanivan S, Krieger MA, Marchini FK, (2017) "The mitogen-activated protein kinase kinase 5 regulates the proliferation and biosynthetic processes in procyclic forms of Trypanosoma brucei." J Proteome Res; PMID: 29043805; doi: 10.1021/acs.jproteome.7b00415; GPMDB: 15.
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Zhang C, Leng W, Sun C, Lu T, Chen Z, Men X, Wang Y, Wang G, Zhen B, Qin J, (2018) "Urine Proteome Profiling Predicts Lung Cancer from Control Cases and Other Tumors." EBioMedicine 30:120–128; PMID: 29576497; doi: 10.1016/j.ebiom.2018.03.009; GPMDB: 557.
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Meng K, Lu S, Yan X, Sun Y, Gao J, Wang Y, Yin X, Sun Z, He QY, (2020) "Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy." J Proteome Res; PMID: 31975592; doi: 10.1021/acs.jproteome.9b00800; GPMDB: 3.
Gonnet J, Poncelet L, Meriaux C, Gonçalves E, Weiss L, Tchitchek N, Pedruzzi E, Soria A, Boccara D, Vogt A, Bonduelle O, Hamm G, Ait-Belkacem R, Stauber J, Fournier I, Wisztorski M, Combadiere B, (2020) "Mechanisms of innate events during skin reaction following intradermal injection of seasonal influenza vaccine." J Proteomics 216:103670; PMID: 31991189; doi: 10.1016/j.jprot.2020.103670; GPMDB: 48.
Veyel D, Wenger K, Broermann A, Bretschneider T, Luippold AH, Krawczyk B, Rist W, Simon E, (2020) "Biomarker discovery for chronic liver diseases by multi-omics - a preclinical case study." Sci Rep 10(1):1314; PMID: 31992752; doi: 10.1038/s41598-020-58030-6; GPMDB: 4.
Lindberg T, de Ávila RI, Zeller KS, Levander F, Eriksson D, Chawade A, Lindstedt M, (2020) "An integrated transcriptomic- and proteomic-based approach to evaluate the human skin sensitization potential of glyphosate and its commercial agrochemical formulations." J Proteomics 217:103647; PMID: 32006680; doi: 10.1016/j.jprot.2020.103647; GPMDB: 21.
Yasuda S, Tsuchiya H, Kaiho A, Guo Q, Ikeuchi K, Endo A, Arai N, Ohtake F, Murata S, Inada T, Baumeister W, Fernández-Busnadiego R, Tanaka K, Saeki Y, (2020) "Stress- and ubiquitylation-dependent phase separation of the proteasome." Nature 578(7794):296–300; PMID: 32025036; doi: 10.1038/s41586-020-1982-9; GPMDB: 6.
Pini T, Parks J, Russ J, Dzieciatkowska M, Hansen KC, Schoolcraft WB, Katz-Jaffe M, (2020) "Obesity significantly alters the human sperm proteome, with potential implications for fertility." J Assist Reprod Genet; PMID: 32026202; doi: 10.1007/s10815-020-01707-8; GPMDB: 20.
Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA, (2020) "Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags." J Proteome Res; PMID: 32027144; doi: 10.1021/acs.jproteome.9b00704; GPMDB: 2.
Eldridge MJG, Pereira JM, Impens F, Hamon MA, (2020) "Active nuclear import of the deacetylase Sirtuin-2 is controlled by its C-terminus and importins." Sci Rep 10(1):2034; PMID: 32042025; doi: 10.1038/s41598-020-58397-6; GPMDB: 6.
Zhao Q, Laverdure JP, Lanoix J, Durette C, Coté C, Bonneil E, Laumont CM, Gendron P, Vincent K, Courcelles M, Lemieux S, Millar DG, Ohashi PS, Thibault P, Perreault C, (2020) "Proteogenomics uncovers a vast repertoire of shared tumor-specific antigens in ovarian cancer." Cancer Immunol Res; PMID: 32047025; doi: 10.1158/2326-6066.CIR-19-0541; GPMDB: 12.
Plum T, Wang X, Rettel M, Krijgsveld J, Feyerabend TB, Rodewald HR, (2020) "Human Mast Cell Proteome Reveals Unique Lineage, Putative Functions, and Structural Basis for Cell Ablation." Immunity; PMID: 32049054; doi: 10.1016/j.immuni.2020.01.012; GPMDB: 12.
Ray S, Valekunja UK, Stangherlin A, Howell SA, Snijders AP, Damodaran G, Reddy AB, (2020) "Circadian rhythms in the absence of the clock gene Bmal1." Science 367(6479):800–806; PMID: 32054765; doi: 10.1126/science.aaw7365; GPMDB: 40.
Saddala MS, Lennikov A, Huang H, (2020) "Placental growth factor regulates the pentose phosphate pathway and antioxidant defense systems in human retinal endothelial cells." J Proteomics 217:103682; PMID: 32058040; doi: 10.1016/j.jprot.2020.103682; GPMDB: 1.
Kosok M, Alli-Shaik A, Bay BH, Gunaratne J, (2020) "Comprehensive Proteomic Characterization Reveals Subclass-Specific Molecular Aberrations within Triple-negative Breast Cancer." iScience 23(2):100868; PMID: 32058975; doi: 10.1016/j.isci.2020.100868; GPMDB: 8.
Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D, Clinical Proteomic Tumor Analysis Consortium., (2020) "Proteogenomic Characterization of Endometrial Carcinoma." Cell 180(4):729–748.e26; PMID: 32059776; doi: 10.1016/j.cell.2020.01.026; GPMDB: 208.
Kalaora S, Lee JS, Barnea E, Levy R, Greenberg P, Alon M, Yagel G, Bar Eli G, Oren R, Peri A, Patkar S, Bitton L, Rosenberg SA, Lotem M, Levin Y, Admon A, Ruppin E, Samuels Y, (2020) "Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma." Nat Commun 11(1):896; PMID: 32060274; doi: 10.1038/s41467-020-14639-9; GPMDB: 30.
Kurimchak AM, Herrera-Montávez C, Brown J, Johnson KJ, Sodi V, Srivastava N, Kumar V, Deihimi S, O'Brien S, Peri S, Mantia-Smaldone GM, Jain A, Winters RM, Cai KQ, Chernoff J, Connolly DC, Duncan JS, (2020) "Functional proteomics interrogation of the kinome identifies MRCKA as a therapeutic target in high-grade serous ovarian carcinoma." Sci Signal 13(619):; PMID: 32071169; doi: 10.1126/scisignal.aax8238; GPMDB: 51.
Touzelet O, Broadbent L, Armstrong SD, Aljabr W, Cloutman-Green E, Power UF, Hiscox JA, (2020) "The secretome profiling of a pediatric airway epithelium infected with hRSV identified aberrant apical/basolateral trafficking and novel immune modulating (CXCL6, CXCL16, CSF3) and antiviral (CEACAM1) proteins." Mol Cell Proteomics; PMID: 32075873; doi: 10.1074/mcp.RA119.001546; GPMDB: 15.
Agudelo Garcia PA, Nagarajan P, Parthun MR, (2020) "Hat1-Dependent Lysine Acetylation Targets Diverse Cellular Functions." J Proteome Res; PMID: 32081014; doi: 10.1021/acs.jproteome.9b00843; GPMDB: 8.
Peters F, Tellkamp F, Brodesser S, Wachsmuth E, Tosetti B, Karow U, Bloch W, Utermöhlen O, Krönke M, Niessen CM, (2020) "Murine Epidermal Ceramide Synthase 4 is a Key Regulator of Skin Barrier Homeostasis." J Invest Dermatol; PMID: 32092351; doi: 10.1016/j.jid.2020.02.006; GPMDB: 40.
Fan Y, Cheng Y, Li Y, Chen B, Wang Z, Wei T, Zhang H, Guo Y, Wang Q, Wei Y, Chen F, Sha J, Guo X, Wang L, (2020) "Phosphoproteomic Analysis of Neonatal Regenerative Myocardium Revealed Important Roles of CHK1 via Activating mTORC1/P70S6K Pathway." Circulation; PMID: 32098494; doi: 10.1161/CIRCULATIONAHA.119.040747; GPMDB: 31.
Zhang J, Tang N, Zhao Y, Zhao R, Fu X, Zhao D, Zhao Y, Huang L, Li C, Qiu Y, Xue B, Fang L, (2020) "Global Phosphoproteomic Analysis Reveals Significant Metabolic Reprogramming in the Termination of Liver Regeneration in Mice." J Proteome Res; PMID: 32105074; doi: 10.1021/acs.jproteome.0c00028; GPMDB: 24.
Kwon OK, Ha YS, Na AY, Chun SY, Kwon TG, Lee JN, Lee S, (2020) "Identification of Novel Prognosis and Prediction Markers in Advanced Prostate Cancer Tissues Based on Quantitative Proteomics." Cancer Genomics Proteomics 17(2):195–208; PMID: 32108042; doi: 10.21873/cgp.20180; GPMDB: 5.
Villaseñor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T, (2020) "ChromID identifies the protein interactome at chromatin marks." Nat Biotechnol; PMID: 32123383; doi: 10.1038/s41587-020-0434-2; GPMDB: 32.
Subbannayya Y, Pinto SM, Mohanty V, Dagamajalu S, Prasad TSK, Murthy KR, (2020) "What Makes Cornea Immunologically Unique and Privileged? Mechanistic Clues from a High-Resolution Proteomic Landscape of the Human Cornea." OMICS 24(3):129–139; PMID: 32125911; doi: 10.1089/omi.2019.0190; GPMDB: 2.
Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH, (2020) "Urine proteomics: Evaluation of different sample preparation workflows for quantitative, reproducible and improved depth of analysis." J Proteome Res; PMID: 32129078; doi: 10.1021/acs.jproteome.9b00772; GPMDB: 16.
Bernatik O, Pejskova P, Vyslouzil D, Hanakova K, Zdrahal Z, Cajanek L, (2020) "Phosphorylation of multiple proteins involved in ciliogenesis by Tau Tubulin kinase 2." Mol Biol Cell :mbcE19060334; PMID: 32129703; doi: 10.1091/mbc.E19-06-0334; GPMDB: 165.
Montellese C, van den Heuvel J, Ashiono C, Dörner K, Melnik A, Jonas S, Zemp I, Picotti P, Gillet LC, Kutay U, (2020) "USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit." Elife; PMID: 32129764; doi: 10.7554/eLife.54435; GPMDB: 18.
Ramat A, Garcia-Silva MR, Jahan C, Naït-Saïdi R, Dufourt J, Garret C, Chartier A, Cremaschi J, Patel V, Decourcelle M, Bastide A, Juge F, Simonelig M, (2020) "The PIWI protein Aubergine recruits eIF3 to activate translation in the germ plasm." Cell Res; PMID: 32132673; doi: 10.1038/s41422-020-0294-9; GPMDB: 12.
Tannous A, Boonen M, Zheng H, Zhao C, Germain CJ, Moore DF, Sleat DE, Jadot M, Lobel P, (2020) "Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics." J Proteome Res 19(4):1718–1730; PMID: 32134668; doi: 10.1021/acs.jproteome.9b00862; GPMDB: 25.
Shayan R, Rinaldi D, Larburu N, Plassart L, Balor S, Bouyssié D, Lebaron S, Marcoux J, Gleizes PE, Plisson-Chastang C, (2020) "Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy." Molecules 25(5):; PMID: 32138239; doi: 10.3390/molecules25051125; GPMDB: 2.
Parker BL, Kiens B, Wojtaszewski JFP, Richter EA, James DE, (2020) "Quantification of exercise-regulated ubiquitin signaling in human skeletal muscle identifies protein modification cross talk via NEDDylation." FASEB J; PMID: 32141134; doi: 10.1096/fj.202000075R; GPMDB: 45.
Wilson JP, Ipsaro JJ, Del Giudice SN, Turna NS, Gauss CM, Dusenbury KH, Marquart K, Rivera KD, Pappin DJ, (2020) "Tryp-N: A Thermostable Protease for the Production of N-terminal Argininyl and Lysinyl Peptides." J Proteome Res 19(4):1459–1469; PMID: 32141294; doi: 10.1021/acs.jproteome.9b00713; GPMDB: 3.
Dietachmayr M, Rathakrishnan A, Karpiuk O, von Zweydorf F, Engleitner T, Fernández-Sáiz V, Schenk P, Ueffing M, Rad R, Eilers M, Gloeckner CJ, Clemm von Hohenberg K, Bassermann F, (2020) "Antagonistic activities of CDC14B and CDK1 on USP9X regulate WT1-dependent mitotic transcription and survival." Nat Commun 11(1):1268; PMID: 32152317; doi: 10.1038/s41467-020-15059-5; GPMDB: 3.
Wan X, Vomund AN, Peterson OJ, Chervonsky AV, Lichti CF, Unanue ER, (2020) "The MHC-II peptidome of pancreatic islets identifies key features of autoimmune peptides." Nat Immunol; PMID: 32152506; doi: 10.1038/s41590-020-0623-7; GPMDB: 9.
Coscia F, Doll S, Bech JM, Schweizer L, Mund A, Lengyel E, Lindebjerg J, Madsen GI, Moreira JMA, Mann M, (2020) "A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis." J Pathol; PMID: 32154592; doi: 10.1002/path.5420; GPMDB: 52.
Yin CF, Kao SC, Hsu CL, Chang YW, Cheung CHY, Huang HC, Juan HF, (2020) "Phosphoproteome Analysis Reveals Dynamic Heat Shock Protein 27 Phosphorylation in Tanshinone IIA-Induced Cell Death." J Proteome Res; PMID: 32154729; doi: 10.1021/acs.jproteome.9b00836; GPMDB: 168.
Chong C, Müller M, Pak H, Harnett D, Huber F, Grun D, Leleu M, Auger A, Arnaud M, Stevenson BJ, Michaux J, Bilic I, Hirsekorn A, Calviello L, Simó-Riudalbas L, Planet E, Lubiński J, Bryśkiewicz M, Wiznerowicz M, Xenarios I, Zhang L, Trono D, Harari A, Ohler U, Coukos G, Bassani-Sternberg M, (2020) "Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes." Nat Commun 11(1):1293; PMID: 32157095; doi: 10.1038/s41467-020-14968-9; GPMDB: 85.
Wegrzyn AB, Herzog K, Gerding A, Kwiatkowski M, Wolters JC, Dolga AM, van Lint AEM, Wanders RJA, Waterham HR, Bakker BM, (2020) "Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease." FEBS J; PMID: 32160399; doi: 10.1111/febs.15292; GPMDB: 71.
Chen L, Shi H, Koftori D, Sekine T, Nicastri A, Ternette N, Bowness P, (2020) "Identification of an unconventional sub-peptidome bound to the Behçet's disease - associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1)." Mol Cell Proteomics; PMID: 32161166; doi: 10.1074/mcp.RA119.001617; GPMDB: 11.
Carnesecchi J, Sigismondo G, Domsch K, Baader CEP, Rafiee MR, Krijgsveld J, Lohmann I, (2020) "Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity." Nat Commun 11(1):1388; PMID: 32170121; doi: 10.1038/s41467-020-15223-x; GPMDB: 36.
Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F, Hernandez-Valladares M, (2020) "Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia." Cancers (Basel) 12(3):; PMID: 32192169; doi: 10.3390/cancers12030709; GPMDB: 214.
Ooi CP, Benz C, Urbaniak MD, (2020) "Phosphoproteomic analysis of mammalian infective Trypanosoma brucei subjected to heat shock suggests atypical mechanisms for thermotolerance." J Proteomics 219:103735; PMID: 32198071; doi: 10.1016/j.jprot.2020.103735; GPMDB: 6.
Guergues J, Wohlfahrt J, Zhang P, Liu B, Stevens SM Jr, (2020) "Deep proteome profiling reveals novel pathways associated with pro-inflammatory and alcohol-induced microglial activation phenotypes." J Proteomics 220:103753; PMID: 32200115; doi: 10.1016/j.jprot.2020.103753; GPMDB: 30.
Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, Paulo JA, (2020) "TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples." Nat Methods 17(4):399–404; PMID: 32203386; doi: 10.1038/s41592-020-0781-4; GPMDB: 9.
Campbell K, Westholm J, Kasvandik S, Di Bartolomeo F, Mormino M, Nielsen J, (2020) "Building blocks are synthesized on demand during the yeast cell cycle." Proc Natl Acad Sci U S A; PMID: 32213592; doi: 10.1073/pnas.1919535117; GPMDB: 105.
Rinfret Robert C, McManus FP, Lamoliatte F, Thibault P, (2020) "Interplay of Ubiquitin-Like Modifiers Following Arsenic Trioxide Treatment." J Proteome Res; PMID: 32223133; doi: 10.1021/acs.jproteome.9b00807; GPMDB: 18.
Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J, (2020) "Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control." EMBO J :e103852; PMID: 32227509; doi: 10.15252/embj.2019103852; GPMDB: 184.
Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E, (2020) "Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy." Genome Med 12(1):32; PMID: 32228647; doi: 10.1186/s13073-020-00731-8; GPMDB: 1017.
Atlasi Y, Jafarnejad SM, Gkogkas CG, Vermeulen M, Sonenberg N, Stunnenberg HG, (2020) "The translational landscape of ground state pluripotency." Nat Commun 11(1):1617; PMID: 32238817; doi: 10.1038/s41467-020-15449-9; GPMDB: 48.
Huang C, Foster SR, Shah AD, Kleifeld O, Canals M, Schittenhelm RB, Stone MJ, (2020) "Phosphoproteomic characterization of the signaling network resulting from activation of chemokine receptor CCR2." J Biol Chem; PMID: 32241914; doi: 10.1074/jbc.RA119.012026; GPMDB: 72.
Morishita Y, Kabil O, Young KZ, Kellogg AP, Chang A, Arvan P, (2020) "Thyrocyte cell survival and adaptation to chronic endoplasmic reticulum stress due to misfolded thyroglobulin." J Biol Chem; PMID: 32241916; doi: 10.1074/jbc.RA120.012656; GPMDB: 1.
Mizukami H, Hathway B, Procopio N, (2020) "Aquatic Decomposition of Mammalian Corpses: A Forensic Proteomic Approach." J Proteome Res; PMID: 32242669; doi: 10.1021/acs.jproteome.0c00060; GPMDB: 22.
Xu G, Fromholt SE, Chakrabarty P, Zhu F, Liu X, Pace MC, Koh J, Golde TE, Levites Y, Lewis J, Borchelt DR, (2020) "Diversity in Aβ deposit morphology and secondary proteome insolubility across models of Alzheimer-type amyloidosis." Acta Neuropathol Commun 8(1):43; PMID: 32252825; doi: 10.1186/s40478-020-00911-y; GPMDB: 57.
Carter SP, Moran AL, Matallanas D, McManus GJ, Blacque OE, Kennedy BN, (2020) "Genetic Deletion of Zebrafish Rab28 Causes Defective Outer Segment Shedding, but Not Retinal Degeneration." Front Cell Dev Biol 8:136; PMID: 32258030; doi: 10.3389/fcell.2020.00136; GPMDB: 12.
Djomehri SI, Gonzalez ME, da Veiga Leprevost F, Tekula SR, Chang HY, White MJ, Cimino-Mathews A, Burman B, Basrur V, Argani P, Nesvizhskii AI, Kleer CG, (2020) "Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors." Nat Commun 11(1):1723; PMID: 32265444; doi: 10.1038/s41467-020-15283-z; GPMDB: 4.
Busso CS, Guidry JJ, Gonzalez JJ, Zorba V, Son LS, Winsauer PJ, Walvekar RR, (2020) "A comprehensive analysis of sialolith proteins and the clinical implications." Clin Proteomics 17:12; PMID: 32265614; doi: 10.1186/s12014-020-09275-w; GPMDB: 1.
Rohlenova K, Goveia J, García-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Vinckier S, Van Bergen T, Ectors N, De Haes P, Wang J, Bolund L, Schoonjans L, Karakach TK, Yang H, Carmeliet G, Liu Y, Thienpont B, Dewerchin M, Eelen G, Li X, Luo Y, Carmeliet P, (2020) "Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis." Cell Metab 31(4):862–877.e14; PMID: 32268117; doi: 10.1016/j.cmet.2020.03.009; GPMDB: 15.
Hoesl C, Zanuttigh E, Fröhlich T, Philippou-Massier J, Krebs S, Blum H, Dahlhoff M, (2020) "The secretome of skin cancer cells activates the mTOR/MYC pathway in healthy keratinocytes and induces tumorigenic properties." Biochim Biophys Acta Mol Cell Res 1867(8):118717; PMID: 32283126; doi: 10.1016/j.bbamcr.2020.118717; GPMDB: 12.
Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B, (2020) "Meltome atlas-thermal proteome stability across the tree of life." Nat Methods 17(5):495–503; PMID: 32284610; doi: 10.1038/s41592-020-0801-4; GPMDB: 31.
Goebel T, Mausbach S, Tuermer A, Eltahir H, Winter D, Gieselmann V, Thelen M, (2020) "Proteaphagy in mammalian cells can function independent of ATG5/ATG7." Mol Cell Proteomics; PMID: 32299840; doi: 10.1074/mcp.RA120.001983; GPMDB: 149.
Chen Z, Wang C, Lei C, Feng X, Li C, Jung SY, Qin J, Chen J, (2020) "Phosphoproteomics Analysis Reveals a Potential Role of CHK1 in Regulation of Innate Immunity through IRF3." J Proteome Res; PMID: 32314919; doi: 10.1021/acs.jproteome.9b00829; GPMDB: 48.
Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A, (2020) "BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain." Cell Syst 10(4):333–350.e14; PMID: 32325033; doi: 10.1016/j.cels.2020.03.003; GPMDB: 578.
Ojalill M, Virtanen N, Rappu P, Siljamäki E, Taimen P, Heino J, (2020) "Interaction between prostate cancer cells and prostate fibroblasts promotes accumulation and proteolytic processing of basement membrane proteins." Prostate 80(9):715–726; PMID: 32364250; doi: 10.1002/pros.23985; GPMDB: 18.
Bekes K, Mitulović G, Meißner N, Resch U, Gruber R, (2020) "Saliva proteomic patterns in patients with molar incisor hypomineralization." Sci Rep 10(1):7560; PMID: 32371984; doi: 10.1038/s41598-020-64614-z; GPMDB: 10.

Retrieved from "http://wiki.thegpm.org/wiki/GPMDB_Data_Sources"

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Revision as of 21:14, 10 June 2020

Contents

Current Public Data Sources

Previous Data Sources

Review process

Data from publications

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@@ Line 5: / Line 5: @@
 The following public data repositories are checked daily for new suitable raw data for reanalysis:
-#PRIDE;
+#ProteomeXchange/PRIDE;
+#JPOST;
 #MASSIVE;
-#PeptideAtlas;
+#PeptideAtlas/PASSEL;
 #ProteomicsDB;
 #The Chorus Project; and
@@ Line 17: / Line 18: @@
 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 be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
+<b>CAUTION</b>: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
+==Data from publications==
+The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of June 7, 2020.
+#Lipton MS, Pasa-Tolic&#39; 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&#39; 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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/15362891 6].
+#Sauer G, K&ouml;rner R, Hanisch A, Ries A, Nigg EA, Sillj&eacute; 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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/15822933 4].
+#Elias JE, Haas W, Faherty BK, Gygi SP,  (2005) &quot;Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations.&quot; <i>Nat Methods</i> <b>2</b>(9):667&ndash;75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16118637 16118637]; doi: [https://dx.doi.org/10.1038/nmeth785 10.1038/nmeth785]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16118637 30].
+#Lee YJ, Rice RH, Lee YM,  (2006) &quot;Proteome analysis of human hair shaft: from protein identification to posttranslational modification.&quot; <i>Mol Cell Proteomics</i> <b>5</b>(5):789&ndash;800; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16446289 16446289]; doi: [https://dx.doi.org/10.1074/mcp.M500278-MCP200 10.1074/mcp.M500278-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16446289 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) &quot;Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus.&quot; <i>Proteomics</i> <b>6</b>(5):1530&ndash;49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/16470658 16470658]; doi: [https://dx.doi.org/10.1002/pmic.200500253 10.1002/pmic.200500253]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16470658 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) &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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/16804162 32].
+#Hamacher M, Apweiler R, Arnold G, Becker A, Bl&uuml;ggel M, Carrette O, Colvis C, Dunn MJ, Fr&ouml;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, St&uuml;hler 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: [https://gpmdb.thegpm.org/data/keyword/16927433 296].
+#Beausoleil SA, Vill&eacute;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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/17164401 314].
+#Tanner S, Shen Z, Ng J, Florea L, Guig&oacute; 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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/17203963 176].
+#Vill&eacute;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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/17431180 2].
+#Lowery DM, Clauser KR, Hjerrild M, Lim D, Alexander J, Kishi K, Ong SE, Gammeltoft S, Carr SA, Yaffe MB,  (2007) &quot;Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.&quot; <i>EMBO J</i> <b>26</b>(9):2262&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17446864 17446864]; doi: [https://dx.doi.org/10.1038/sj.emboj.7601683 10.1038/sj.emboj.7601683]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17446864 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) &quot;A high-quality catalog of the Drosophila melanogaster proteome.&quot; <i>Nat Biotechnol</i> <b>25</b>(5):576&ndash;83; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17450130 17450130]; doi: [https://dx.doi.org/10.1038/nbt1300 10.1038/nbt1300]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17450130 1907].
+#Wu L, Hwang SI, Rezaul K, Lu LJ, Mayya V, Gerstein M, Eng JK, Lundgren DH, Han DK,  (2007) &quot;Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling.&quot; <i>Mol Cell Proteomics</i> <b>6</b>(8):1343&ndash;53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17519225 17519225]; doi: [https://dx.doi.org/10.1074/mcp.M700017-MCP200 10.1074/mcp.M700017-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17519225 2299].
+#Au CE, Bell AW, Gilchrist A, Hiding J, Nilsson T, Bergeron JJ,  (2007) &quot;Organellar proteomics to create the cell map.&quot; <i>Curr Opin Cell Biol</i> <b>19</b>(4):376&ndash;85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17689063 17689063]; doi: [https://dx.doi.org/10.1016/j.ceb.2007.05.004 10.1016/j.ceb.2007.05.004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17689063 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) &quot;Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer.&quot; <i>J Proteome Res</i> <b>6</b>(10):3962&ndash;75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17711321 17711321]; doi: [https://dx.doi.org/10.1021/pr070202v 10.1021/pr070202v]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17711321 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) &quot;Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors.&quot; <i>Nat Biotechnol</i> <b>25</b>(9):1035&ndash;44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17721511 17721511]; doi: [https://dx.doi.org/10.1038/nbt1328 10.1038/nbt1328]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17721511 729].
+#Padliya ND, Garrett WM, Campbell KB, Tabb DL, Cooper B,  (2007) &quot;Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.&quot; <i>Proteomics</i> <b>7</b>(21):3932&ndash;42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/17922518 17922518]; doi: [https://dx.doi.org/10.1002/pmic.200700419 10.1002/pmic.200700419]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17922518 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) &quot;Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.&quot; <i>Cell</i> <b>131</b>(6):1190&ndash;203; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18083107 18083107]; doi: [https://dx.doi.org/10.1016/j.cell.2007.11.025 10.1016/j.cell.2007.11.025]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18083107 104].
+#Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD,  (2008) &quot;Proteomics analysis of the causative agent of typhoid fever.&quot; <i>J Proteome Res</i> <b>7</b>(2):546&ndash;57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18166006 18166006]; doi: [https://dx.doi.org/10.1021/pr070434u 10.1021/pr070434u]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18166006 313].
+#Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ,  (2008) &quot;Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data.&quot; <i>Anal Chem</i> <b>80</b>(4):961&ndash;71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18189369 18189369]; doi: [https://dx.doi.org/10.1021/ac701649e 10.1021/ac701649e]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18189369 12].
+#Stevens SM Jr, Duncan RS, Koulen P, Prokai L,  (2008) &quot;Proteomic analysis of mouse brain microsomes: identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system.&quot; <i>J Proteome Res</i> <b>7</b>(3):1046&ndash;54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18271522 18271522]; doi: [https://dx.doi.org/10.1021/pr7006279 10.1021/pr7006279]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18271522 4].
+#Yocum AK, Gratsch TE, Leff N, Strahler JR, Hunter CL, Walker AK, Michailidis G, Omenn GS, O&#39;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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/18307296 148].
+#Zhai B, Vill&eacute;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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/18361515 102].
+#Sim&oacute; 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: [https://gpmdb.thegpm.org/data/keyword/18399644 19].
+#Bachi A, Sim&oacute; C, Restuccia U, Guerrier L, Fortis F, Boschetti E, Masseroli M, Righetti PG,  (2008) &quot;Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 2. Behavior of resins containing individual amino acids.&quot; <i>Anal Chem</i> <b>80</b>(10):3557&ndash;65; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18410134 18410134]; doi: [https://dx.doi.org/10.1021/ac8001353 10.1021/ac8001353]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18410134 2].
+#Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S,  (2008) &quot;Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.&quot; <i>Science</i> <b>320</b>(5878):938&ndash;41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18436743 18436743]; doi: [https://dx.doi.org/10.1126/science.1157956 10.1126/science.1157956]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18436743 28].
+#Ji H, Erfani N, Tauro BJ, Kapp EA, Zhu HJ, Moritz RL, Lim JW, Simpson RJ,  (2008) &quot;Difference gel electrophoresis analysis of Ras-transformed fibroblast cell-derived exosomes.&quot; <i>Electrophoresis</i> <b>29</b>(12):2660&ndash;71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18494037 18494037]; doi: [https://dx.doi.org/10.1002/elps.200800015 10.1002/elps.200800015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18494037 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) &quot;Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis.&quot; <i>Mol Cell Proteomics</i> <b>7</b>(9):1651&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18504258 18504258]; doi: [https://dx.doi.org/10.1074/mcp.M700155-MCP200 10.1074/mcp.M700155-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18504258 6].
+#Lemeer S, Jopling C, Gouw J, Mohammed S, Heck AJ, Slijper M, den Hertog J,  (2008) &quot;Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos.&quot; <i>Mol Cell Proteomics</i> <b>7</b>(11):2176&ndash;87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18550893 18550893]; doi: [https://dx.doi.org/10.1074/mcp.M800081-MCP200 10.1074/mcp.M800081-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18550893 31].
+#Sodek KL, Evangelou AI, Ignatchenko A, Agochiya M, Brown TJ, Ringuette MJ, Jurisica I, Kislinger T,  (2008) &quot;Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT).&quot; <i>Mol Biosyst</i> <b>4</b>(7):762&ndash;73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/18563251 18563251]; doi: [https://dx.doi.org/10.1039/b717542f 10.1039/b717542f]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/18563251 252].
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+#Helbig AO, Rosati S, Pijnappel PW, van Breukelen B, Timmers MH, Mohammed S, Slijper M, Heck AJ,  (2010) &quot;Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.&quot; <i>BMC Genomics</i> <b>11</b>:685; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21126336 21126336]; doi: [https://dx.doi.org/10.1186/1471-2164-11-685 10.1186/1471-2164-11-685]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21126336 10].
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+#Rivera FE, Miller HK, Kolar SL, Stevens SM Jr, Shaw LN,  (2012) &quot;The impact of CodY on virulence determinant production in community-associated methicillin-resistant Staphylococcus aureus.&quot; <i>Proteomics</i> <b>12</b>(2):263&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22106056 22106056]; doi: [https://dx.doi.org/10.1002/pmic.201100298 10.1002/pmic.201100298]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/22106056 6].
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+#Murray CI, Uhrigshardt H, O&#39;Meally RN, Cole RN, Van Eyk JE,  (2012) &quot;Identification and quantification of S-nitrosylation by cysteine reactive tandem mass tag switch assay.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(2):M111.013441; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22126794 22126794]; doi: [https://dx.doi.org/10.1074/mcp.M111.013441 10.1074/mcp.M111.013441]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/22126794 3].
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+#Choi DS, Yang JS, Choi EJ, Jang SC, Park S, Kim OY, Hwang D, Kim KP, Kim YK, Kim S, Gho YS,  (2012) &quot;The protein interaction network of extracellular vesicles derived from human colorectal cancer cells.&quot; <i>J Proteome Res</i> <b>11</b>(2):1144&ndash;51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22149170 22149170]; doi: [https://dx.doi.org/10.1021/pr200842h 10.1021/pr200842h]; GPMDB: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/22159717 98].
+#Michalski A, Damoc E, Lange O, Denisov E, Nolting D, M&uuml;ller M, Viner R, Schwartz J, Remes P, Belford M, Dunyach JJ, Cox J, Horning S, Mann M, Makarov A,  (2012) &quot;Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):O111.013698; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22159718 22159718]; doi: [https://dx.doi.org/10.1074/mcp.O111.013698 10.1074/mcp.O111.013698]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/22159718 22].
+#Martins-de-Souza D, Guest PC, Guest FL, Bauder C, Rahmoune H, Pietsch S, Roeber S, Kretzschmar H, Mann D, Baborie A, Bahn S,  (2012) &quot;Characterization of the human primary visual cortex and cerebellum proteomes using shotgun mass spectrometry-data-independent analyses.&quot; <i>Proteomics</i> <b>12</b>(3):500&ndash;4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22162416 22162416]; doi: [https://dx.doi.org/10.1002/pmic.201100476 10.1002/pmic.201100476]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/22162416 26].
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+#Sharma K, Vabulas RM, Macek B, Pinkert S, Cox J, Mann M, Hartl FU,  (2012) &quot;Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response.&quot; <i>Mol Cell Proteomics</i> <b>11</b>(3):M111.014654; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22167270 22167270]; doi: [https://dx.doi.org/10.1074/mcp.M111.014654 10.1074/mcp.M111.014654]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/22167270 41].
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+#Fanayan S, Smith JT, Lee LY, Yan F, Snyder M, Hancock WS, Nice E,  (2013) &quot;Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.&quot; <i>J Proteome Res</i> <b>12</b>(4):1732&ndash;42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23458625 23458625]; doi: [https://dx.doi.org/10.1021/pr3010869 10.1021/pr3010869]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23458625 136].
+#Rao SA, Carolan JC, Wilkinson TL,  (2013) &quot;Proteomic profiling of cereal aphid saliva reveals both ubiquitous and adaptive secreted proteins.&quot; <i>PLoS One</i> <b>8</b>(2):e57413; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23460852 23460852]; doi: [https://dx.doi.org/10.1371/journal.pone.0057413 10.1371/journal.pone.0057413]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23460852 16].
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+#Koch H, Busto ME, Kramer K, M&eacute;dard 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: [https://gpmdb.thegpm.org/data/keyword/25963923 18].
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+#Sj&ouml;lin-Goodfellow H, Frushicheva MP, Ji Q, Cheng DA, Kadlecek TA, Cantor AJ, Kuriyan J, Chakraborty AK, Salomon AR, Weiss A,  (2015) &quot;The catalytic activity of the kinase ZAP-70 mediates basal signaling and negative feedback of the T cell receptor pathway.&quot; <i>Sci Signal</i> <b>8</b>(377):ra49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25990959 25990959]; doi: [https://dx.doi.org/10.1126/scisignal.2005596 10.1126/scisignal.2005596]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25990959 20].
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+#Chen Y, Yang F, Sun Z, Wang Q, Mi K, Deng H,  (2015) &quot;Proteomic Analysis of Drug-Resistant Mycobacteria: Co-Evolution of Copper and INH Resistance.&quot; <i>PLoS One</i> <b>10</b>(6):e0127788; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26035302 26035302]; doi: [https://dx.doi.org/10.1371/journal.pone.0127788 10.1371/journal.pone.0127788]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26035302 1].
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+#Helou YA, Petrashen AP, Salomon AR,  (2015) &quot;Vav1 Regulates T-Cell Activation through a Feedback Mechanism and Crosstalk between the T-Cell Receptor and CD28.&quot; <i>J Proteome Res</i> <b>14</b>(7):2963&ndash;75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26043137 26043137]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00340 10.1021/acs.jproteome.5b00340]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26043137 40].
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+#Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ,  (2015) &quot;The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins.&quot; <i>Mol Cell</i> <b>59</b>(1):35&ndash;49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26051182 26051182]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.04.026 10.1016/j.molcel.2015.04.026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26051182 54].
+#Sethi MK, Thaysen-Andersen M, Kim H, Park CK, Baker MS, Packer NH, Paik YK, Hancock WS, Fanayan S,  (2015) &quot;Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis.&quot; <i>J Proteomics</i> <b>126</b>:54&ndash;67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26054784 26054784]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.037 10.1016/j.jprot.2015.05.037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26054784 15].
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+#Kwon OK, Lee W, Kim SJ, Lee YM, Lee JY, Kim JY, Bae JS, Lee S,  (2015) &quot;In-depth proteomics approach of secretome to identify novel biomarker for sepsis in LPS-stimulated endothelial cells.&quot; <i>Electrophoresis</i> <b>36</b>(23):2851&ndash;8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26257168 26257168]; doi: [https://dx.doi.org/10.1002/elps.201500198 10.1002/elps.201500198]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26257168 4].
+#He P, Zhao L, Zhu L, Weinman EJ, De Giorgio R, Koval M, Srinivasan S, Yun CC,  (2015) &quot;Restoration of Na+/H+ exchanger NHE3-containing macrocomplexes ameliorates diabetes-associated fluid loss.&quot; <i>J Clin Invest</i> <b>125</b>(9):3519&ndash;31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26258413 26258413]; doi: [https://dx.doi.org/10.1172/JCI79552 10.1172/JCI79552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26258413 20].
+#Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan EC, Zhou L,  (2015) &quot;Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress.&quot; <i>J Proteome Res</i> <b>14</b>(9):3982&ndash;95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26260330 26260330]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00443 10.1021/acs.jproteome.5b00443]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26260330 3].
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+#Humphrey SJ, Azimifar SB, Mann M,  (2015) &quot;High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics.&quot; <i>Nat Biotechnol</i> <b>33</b>(9):990&ndash;5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26280412 26280412]; doi: [https://dx.doi.org/10.1038/nbt.3327 10.1038/nbt.3327]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26280412 199].
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+#Titz B, Sewer A, Schneider T, Elamin A, Martin F, Dijon S, Luettich K, Guedj E, Vuillaume G, Ivanov NV, Peck MJ, Chaudhary NI, Hoeng J, Peitsch MC,  (2015) &quot;Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects.&quot; <i>J Proteomics</i> <b>128</b>:306&ndash;20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26306861 26306861]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.08.009 10.1016/j.jprot.2015.08.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26306861 120].
+#Yang CR, Raghuram V, Emamian M, Sandoval PC, Knepper MA,  (2015) &quot;Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling.&quot; <i>Am J Physiol Cell Physiol</i> <b>309</b>(12):C799&ndash;812; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26310817 26310817]; doi: [https://dx.doi.org/10.1152/ajpcell.00214.2015 10.1152/ajpcell.00214.2015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26310817 257].
+#Deeb SJ, Tyanova S, Hummel M, Schmidt-Supprian M, Cox J, Mann M,  (2015) &quot;Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles.&quot; <i>Mol Cell Proteomics</i> <b>14</b>(11):2947&ndash;60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26311899 26311899]; doi: [https://dx.doi.org/10.1074/mcp.M115.050245 10.1074/mcp.M115.050245]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26311899 20].
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+#Grosche A, Hauser A, Lepper MF, Mayo R, von Toerne C, Merl-Pham J, Hauck SM,  (2016) &quot;The Proteome of Native Adult M&uuml;ller Glial Cells From Murine Retina.&quot; <i>Mol Cell Proteomics</i> <b>15</b>(2):462&ndash;80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26324419 26324419]; doi: [https://dx.doi.org/10.1074/mcp.M115.052183 10.1074/mcp.M115.052183]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26324419 40].
+#Chu XL, Feng MG, Ying SH,  (2016) &quot;Qualitative ubiquitome unveils the potential significances of protein lysine ubiquitination in hyphal growth of Aspergillus nidulans.&quot; <i>Curr Genet</i> <b>62</b>(1):191&ndash;201; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26328806 26328806]; doi: [https://dx.doi.org/10.1007/s00294-015-0517-7 10.1007/s00294-015-0517-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26328806 1].
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+#Xu B, Tian R, Wang X, Zhan S, Wang R, Guo Y, Ge W,  (2016) &quot;Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury.&quot; <i>Brain Res</i> <b>1642</b>:344&ndash;52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067185 27067185]; doi: [https://dx.doi.org/10.1016/j.brainres.2016.04.008 10.1016/j.brainres.2016.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27067185 20].
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+#Hakimi O, Ternette N, Murphy R, Kessler BM, Carr A,  (2017) &quot;A quantitative label-free analysis of the extracellular proteome of human supraspinatus tendon reveals damage to the pericellular and elastic fibre niches in torn and aged tissue.&quot; <i>PLoS One</i> <b>12</b>(5):e0177656; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28542244 28542244]; doi: [https://dx.doi.org/10.1371/journal.pone.0177656 10.1371/journal.pone.0177656]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28542244 116].
+#Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke DM, Parker GJ, Rice RH,  (2017) &quot;Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides.&quot; <i>Proteomics</i> <b>17</b>(13-14):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28544375 28544375]; doi: [https://dx.doi.org/10.1002/pmic.201600462 10.1002/pmic.201600462]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28544375 24].
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+#Li JY, Cai F, Ye XG, Liang JS, Li JK, Wu MY, Zhao D, Jiang ZD, You ZY, Zhong BX,  (2017) &quot;Comparative Proteomic Analysis of Posterior Silk Glands of Wild and Domesticated Silkworms Reveals Functional Evolution during Domestication.&quot; <i>J Proteome Res</i> <b>16</b>(7):2495&ndash;2507; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28569067 28569067]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00077 10.1021/acs.jproteome.7b00077]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28569067 72].
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+#Sun C, De Mello V, Mohamed A, Ortuste Quiroga HP, Garcia-Munoz A, Al Bloshi A, Tremblay AM, von Kriegsheim A, Collie-Duguid E, Vargesson N, Matallanas D, Wackerhage H, Zammit PS,  (2017) &quot;Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function.&quot; <i>Stem Cells</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28589555 28589555]; doi: [https://dx.doi.org/10.1002/stem.2652 10.1002/stem.2652]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28589555 36].
+#Zhang J, Lu S, Zhou Y, Meng K, Chen Z, Cui Y, Shi Y, Wang T, He QY,  (2017) &quot;Motile hepatocellular carcinoma cells preferentially secret sugar metabolism regulatory proteins via exosomes.&quot; <i>Proteomics</i> <b>17</b>(13-14):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28590090 28590090]; doi: [https://dx.doi.org/10.1002/pmic.201700103 10.1002/pmic.201700103]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28590090 6].
+#Jensen SR, Schoof EM, Wheeler SE, Hvid H, Ahnfelt-R&oslash;nne J, Hansen BF, Nishimura E, Olsen GS, Kislinger T, Brubaker PL,  (2017) &quot;Quantitative Proteomics of Intestinal Mucosa From Male Mice Lacking Intestinal Epithelial Insulin Receptors.&quot; <i>Endocrinology</i> <b>158</b>(8):2470&ndash;2485; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28591806 28591806]; doi: [https://dx.doi.org/10.1210/en.2017-00194 10.1210/en.2017-00194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28591806 10].
+#Pearson LJ, Klaharn IY, Thongsawang B, Manuprasert W, Saejew T, Somparn P, Chuengsaman P, Kanjanabuch T, Pisitkun T,  (2017) &quot;Multiple extracellular vesicle types in peritoneal dialysis effluent are prominent and contain known biomarkers.&quot; <i>PLoS One</i> <b>12</b>(6):e0178601; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28594924 28594924]; doi: [https://dx.doi.org/10.1371/journal.pone.0178601 10.1371/journal.pone.0178601]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28594924 90].
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+#Lapek JD Jr, Lewinski MK, Wozniak JM, Guatelli J, Gonzalez DJ,  (2017) &quot;Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Vpr.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28606917 28606917]; doi: [https://dx.doi.org/10.1074/mcp.M116.066019 10.1074/mcp.M116.066019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28606917 4].
+#Brocard L, Immel F, Coulon D, Esnay N, Tuphile K, Pascal S, Claverol S, Fouillen L, Bessoule JJ, Br&eacute;h&eacute;lin C,  (2017) &quot;Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions.&quot; <i>Front Plant Sci</i> <b>8</b>:894; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28611809 28611809]; doi: [https://dx.doi.org/10.3389/fpls.2017.00894 10.3389/fpls.2017.00894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28611809 3].
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+#Murgia M, Toniolo L, Nagaraj N, Ciciliot S, Vindigni V, Schiaffino S, Reggiani C, Mann M,  (2017) &quot;Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging.&quot; <i>Cell Rep</i> <b>19</b>(11):2396&ndash;2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28614723 28614723]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.05.054 10.1016/j.celrep.2017.05.054]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28614723 174].
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+#Marx H, Hahne H, Ulbrich SE, Schnieke A, Rottmann O, Frishman D, Kuster B,  (2017) &quot;Annotation of the Domestic Pig Genome by Quantitative Proteogenomics.&quot; <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28625053 28625053]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00184 10.1021/acs.jproteome.7b00184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28625053 181].
+#Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM,  (2017) &quot;Colorectal Cancer Cell Line Proteomes are Representative of Primary Tumors and Predict Drug Sensitivity.&quot; <i>Gastroenterology</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28625833 28625833]; doi: [https://dx.doi.org/10.1053/j.gastro.2017.06.008 10.1053/j.gastro.2017.06.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28625833 44].
+#Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T,  (2017) &quot;Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma.&quot; <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28626882 28626882]; doi: [https://dx.doi.org/10.1002/prca.201700014 10.1002/prca.201700014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28626882 56].
+#Qin G, Dang M, Gao H, Wang H, Luo F, Chen R,  (2017) &quot;Deciphering the protein-protein interaction network regulating hepatocellular carcinoma metastasis.&quot; <i>Biochim Biophys Acta</i> <b>1865</b>(9):1114&ndash;1122; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28627476 28627476]; doi: [https://dx.doi.org/10.1016/j.bbapap.2017.06.005 10.1016/j.bbapap.2017.06.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28627476 6].
+#Sung E, Kwon OK, Lee JM, Lee S,  (2017) &quot;Proteomics approach to identify novel metastatic bone markers from the secretome of PC-3 prostate cancer cells.&quot; <i>Electrophoresis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28627741 28627741]; doi: [https://dx.doi.org/10.1002/elps.201700052 10.1002/elps.201700052]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28627741 2].
+#Loke I, &Oslash;stergaard O, Heegaard NHH, Packer NH, Thaysen-Andersen M,  (2017) &quot;Paucimannose-Rich <i>N</i>-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28630087 28630087]; doi: [https://dx.doi.org/10.1074/mcp.M116.066746 10.1074/mcp.M116.066746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28630087 118].
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+#Henriet E, Abou Hammoud A, Dupuy JW, Dartigues B, Ezzoukry Z, Dugot-Senant N, Leste-Lasserre T, Pallares-Lupon N, Nikolski M, Le Bail B, Blanc JF, Balabaud C, Bioulac-Sage P, Raymond AA, Saltel F,  (2017) &quot;Argininosuccinate synthase 1 (ASS1): A marker of unclassified hepatocellular adenoma and high bleeding risk.&quot; <i>Hepatology</i> <b>66</b>(6):2016&ndash;2028; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28646562 28646562]; doi: [https://dx.doi.org/10.1002/hep.29336 10.1002/hep.29336]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28646562 124].
+#Gu Y, Albuquerque CP, Braas D, Zhang W, Villa GR, Bi J, Ikegami S, Masui K, Gini B, Yang H, Gahman TC, Shiau AK, Cloughesy TF, Christofk HR, Zhou H, Guan KL, Mischel PS,  (2017) &quot;mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT.&quot; <i>Mol Cell</i> <b>67</b>(1):128&ndash;138.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648777 28648777]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.030 10.1016/j.molcel.2017.05.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28648777 2].
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+#Offenburger SL, Bensaddek D, Murillo AB, Lamond AI, Gartner A,  (2017) &quot;Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development.&quot; <i>Sci Rep</i> <b>7</b>(1):4314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28659600 28659600]; doi: [https://dx.doi.org/10.1038/s41598-017-04375-4 10.1038/s41598-017-04375-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28659600 289].
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