GPMDB Data Sources

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Revision as of 16:55, 12 May 2019

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Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.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 May 12, 2019.

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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Byron A, Askari JA, Humphries JD, Jacquemet G, Koper EJ, Warwood S, Choi CK, Stroud MJ, Chen CS, Knight D, Humphries MJ, (2015) "A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting." Nat Commun 6:6135; PMID: 25609142; doi: 10.1038/ncomms7135; GPMDB: 237.
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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.
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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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Peffers MJ, Collins J, Fang Y, Goljanek-Whysall K, Rushton M, Loughlin J, Proctor C, Clegg PD, (2016) "Age-related changes in mesenchymal stem cells identified using a multi-omics approach." Eur Cell Mater 31:136–59; PMID: 26853623; GPMDB: 8.
Billing AM, Ben Hamidane H, Dib SS, Cotton RJ, Bhagwat AM, Kumar P, Hayat S, Yousri NA, Goswami N, Suhre K, Rafii A, Graumann J, (2016) "Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers." Sci Rep 6:21507; PMID: 26857143; doi: 10.1038/srep21507; GPMDB: 9.
Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C, (2016) "Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes." Proc Natl Acad Sci U S A 113(8):E968–77; PMID: 26858453; doi: 10.1073/pnas.1521230113; GPMDB: 56.
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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.
Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." Int J Med Microbiol 306(3):131–40; PMID: 26996810; doi: 10.1016/j.ijmm.2016.02.004; GPMDB: 300.
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Liñeiro E, Chiva C, Cantoral JM, Sabido E, Fernández-Acero FJ, (2016) "Phosphoproteome analysis of B. cinerea in response to different plant-based elicitors." J Proteomics 139:84–94; PMID: 27003611; doi: 10.1016/j.jprot.2016.03.019; GPMDB: 8.
Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher DF, Coon JJ, (2016) "The Peripheral Blood Eosinophil Proteome." J Proteome Res 15(5):1524–33; PMID: 27005946; doi: 10.1021/acs.jproteome.6b00006; GPMDB: 45.
Wilson MC, Trakarnsanga K, Heesom KJ, Cogan N, Green C, Toye AM, Parsons SF, Anstee DJ, Frayne J, (2016) "Comparison of the Proteome of Adult and Cord Erythroid Cells, and Changes in the Proteome Following Reticulocyte Maturation." Mol Cell Proteomics 15(6):1938–46; PMID: 27006477; doi: 10.1074/mcp.M115.057315; GPMDB: 2.
Sunitha B, Gayathri N, Kumar M, Keshava Prasad TS, Nalini A, Padmanabhan B, Srinivas Bharath MM, (2016) "Muscle biopsies from human muscle diseases with myopathic pathology reveal common alterations in mitochondrial function." J Neurochem 138(1):174–91; PMID: 27015874; doi: 10.1111/jnc.13626; GPMDB: 1.
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Karunakaran KP, Yu H, Jiang X, Chan Q, Goldberg MF, Jenkins MK, Foster LJ, Brunham RC, (2017) "Identification of MHC-Bound Peptides from Dendritic Cells Infected with Salmonella enterica Strain SL1344: Implications for a Nontyphoidal Salmonella Vaccine." J Proteome Res 16(1):298–306; PMID: 27802388; doi: 10.1021/acs.jproteome.6b00926; GPMDB: 3.
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.
Loroch S, Trabold K, Gambaryan S, Reiß C, Schwierczek K, Fleming I, Sickmann A, Behnisch W, Zieger B, Zahedi RP, Walter U, Jurk K, (2017) "Alterations of the platelet proteome in type I Glanzmann thrombasthenia caused by different homozygous delG frameshift mutations in ITGA2B." Thromb Haemost 117(3):556–569; PMID: 28078347; doi: 10.1160/TH16-07-0515; GPMDB: 20.
Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." Mol Syst Biol 13(1):906; PMID: 28082348; GPMDB: 521.
Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." Mol Cell Proteomics; PMID: 28087593; doi: 10.1074/mcp.M116.062448; GPMDB: 3.
Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra J, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm-Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M, (2017) "Membrane-depolarizing channel blockers induce selective glioma cell death by impairing nutrient transport and unfolded protein/amino acid responses." Cancer Res; PMID: 28087597; doi: 10.1158/0008-5472.CAN-16-2274; GPMDB: 6.
Gao Y, Chen Y, Zhan S, Zhang W, Xiong F, Ge W, (2017) "Comprehensive proteome analysis of lysosomes reveals the diverse function of macrophages in immune responses." Oncotarget 8(5):7420–7440; PMID: 28088779; doi: 10.18632/oncotarget.14558; GPMDB: 2.
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Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY, Butter F, (2017) "The developmental proteome of Drosophila melanogaster." Genome Res; PMID: 28381612; doi: 10.1101/gr.213694.116; GPMDB: 124.
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Mohr S, Doebele C, Comoglio F, Berg T, Beck J, Bohnenberger H, Alexe G, Corso J, Ströbel P, Wachter A, Beissbarth T, Schnütgen F, Cremer A, Haetscher N, Göllner S, Rouhi A, Palmqvist L, Rieger MA, Schroeder T, Bönig H, Müller-Tidow C, Kuchenbauer F, Schütz E, Green AR, Urlaub H, Stegmaier K, Humphries RK, Serve H, Oellerich T, (2017) "Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia." Cancer Cell 31(4):549–562.e11; PMID: 28399410; doi: 10.1016/j.ccell.2017.03.001; GPMDB: 30.
Rinschen MM, Grahammer F, Hoppe AK, Kohli P, Hagmann H, Kretz O, Bertsch S, Höhne M, Göbel H, Bartram MP, Gandhirajan RK, Krüger M, Brinkkoetter PT, Huber TB, Kann M, Wickström SA, Benzing T, Schermer B, (2017) "YAP-mediated mechanotransduction determines the podocyte's response to damage." Sci Signal 10(474):; PMID: 28400537; doi: 10.1126/scisignal.aaf8165; GPMDB: 23.
Müller MM, Lehmann R, Klassert TE, Reifenstein S, Conrad T, Moore C, Kuhn A, Behnert A, Guthke R, Driesch D, Slevogt H, (2017) "Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression." Sci Rep 7(1):838; PMID: 28404994; doi: 10.1038/s41598-017-00828-y; GPMDB: 138.
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Kathiriya JJ, Nakra N, Nixon J, Patel PS, Vaghasiya V, Alhassani A, Tian Z, Allen-Gipson D, Davé V, (2017) "Galectin-1 inhibition attenuates profibrotic signaling in hypoxia-induced pulmonary fibrosis." Cell Death Discov 3:17010; PMID: 28417017; doi: 10.1038/cddiscovery.2017.10; GPMDB: 3.
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Mendoza-Viveros L, Chiang CK, Ong JLK, Hegazi S, Cheng AH, Bouchard-Cannon P, Fana M, Lowden C, Zhang P, Bothorel B, Michniewicz MG, Magill ST, Holmes MM, Goodman RH, Simonneaux V, Figeys D, Cheng HM, (2017) "miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock." Cell Rep 19(3):505–520; PMID: 28423315; doi: 10.1016/j.celrep.2017.03.057; GPMDB: 128.
Maus RLG, Jakub JW, Nevala WK, Christensen TA, Noble-Orcutt K, Sachs Z, Hieken TJ, Markovic SN, (2017) "Human Melanoma-Derived Extracellular Vesicles Regulate Dendritic Cell Maturation." Front Immunol 8:358; PMID: 28424693; doi: 10.3389/fimmu.2017.00358; GPMDB: 18.
Treiber T, Treiber N, Plessmann U, Harlander S, Daiß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G, (2017) "A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis." Mol Cell 66(2):270–284.e13; PMID: 28431233; doi: 10.1016/j.molcel.2017.03.014; GPMDB: 3033.
Beyene GT, Kalayou S, Riaz T, Tonjum T, (2017) "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis." BMC Microbiol 17(1):96; PMID: 28431522; doi: 10.1186/s12866-017-1004-8; GPMDB: 108.
Xu B, Gao Y, Zhan S, Ge W, (2017) "Quantitative proteomic profiling for clarification of the crucial roles of lysosomes in microbial infections." Mol Immunol 87:122–131; PMID: 28433889; doi: 10.1016/j.molimm.2017.04.002; GPMDB: 2.
Clulow JA, Storck EM, Lanyon-Hogg T, Kalesh KA, Jones LH, Tate EW, (2017) "Competition-based, quantitative chemical proteomics in breast cancer cells identifies new target profiles for sulforaphane." Chem Commun (Camb) 53(37):5182–5185; PMID: 28439590; doi: 10.1039/c6cc08797c; GPMDB: 32.
Yeung ATY, Hale C, Lee AH, Gill EE, Bushell W, Parry-Smith D, Goulding D, Pickard D, Roumeliotis T, Choudhary J, Thomson N, Skarnes WC, Dougan G, Hancock REW, (2017) "Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis." Nat Commun 8:15013; PMID: 28440293; doi: 10.1038/ncomms15013; GPMDB: 1.
Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB, (2017) "Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity." Environ Microbiol; PMID: 28447389; doi: 10.1111/1462-2920.13770; GPMDB: 20.
Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." Mol Cell Proteomics; PMID: 28455291; doi: 10.1074/mcp.M116.058321; GPMDB: 60.
Aviner R, Hofmann S, Elman T, Shenoy A, Geiger T, Elkon R, Ehrlich M, Elroy-Stein O, (2017) "Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis." Nucleic Acids Res 45(10):5945–5957; PMID: 28460002; doi: 10.1093/nar/gkx326; GPMDB: 15.
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van Aalderen MC, van den Biggelaar M, Remmerswaal EBM, van Alphen FPJ, Meijer AB, Ten Berge IJM, van Lier RAW, (2017) "Label-free Analysis of CD8⁺ T Cell Subset Proteomes Supports a Progressive Differentiation Model of Human-Virus-Specific T Cells." Cell Rep 19(5):1068–1079; PMID: 28467900; doi: 10.1016/j.celrep.2017.04.014; GPMDB: 84.
Tello-Lafoz M, Martínez-Martínez G, Rodríguez-Rodríguez C, Albar JP, Huse M, Gharbi S, Merida I, (2017) "SNX27 interactome in T lymphocytes identifies ZO-2 dynamic redistribution at the immune synapse." Traffic; PMID: 28477369; doi: 10.1111/tra.12492; GPMDB: 57.
Ozdian T, Holub D, Maceckova Z, Varanasi L, Rylova G, Rehulka J, Vaclavkova J, Slavik H, Moudry P, Znojek P, Stankova J, de Sanctis JB, Hajduch M, Dzubak P, (2017) "Proteomic profiling reveals DNA damage, nucleolar and ribosomal stress are the main responses to oxaliplatin treatment in cancer cells." J Proteomics; PMID: 28478306; doi: 10.1016/j.jprot.2017.05.005; GPMDB: 63.
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Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ, (2017) "Common genetic variation drives molecular heterogeneity in human iPSCs." Nature; PMID: 28489815; doi: 10.1038/nature22403; GPMDB: 72.
Jahn A, Rane G, Paszkowski-Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño-Vallejo JA, Kumar AP, Buchholz F, Butter F, Kappei D, (2017) "ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator." EMBO Rep 18(6):929–946; PMID: 28500257; doi: 10.15252/embr.201744095; GPMDB: 35.
Kramer DA, Eldeeb MA, Wuest M, Mercer J, Fahlman RP, (2017) "Proteomic characterization of EL4 lymphoma derived tumors upon chemotherapy treatment reveals potential roles for lysosomes and caspase-6 during tumor cell death in vivo." Proteomics; PMID: 28508578; doi: 10.1002/pmic.201700060; GPMDB: 150.
Peng W, Zhang Y, Zhu R, Mechref Y, (2017) "Comparative Membrane Proteomics Analyses of Breast Cancer Cell Lines to Understand the Molecular Mechanism of Breast Cancer Brain Metastasis." Electrophoresis; PMID: 28523741; doi: 10.1002/elps.201700027; GPMDB: 18.
Zai X, Yang Q, Liu K, Li R, Qian M, Zhao T, Li Y, Yin Y, Dong D, Fu L, Li S, Xu J, Chen W, (2017) "A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M." BMC Genomics 18(1):402; PMID: 28535754; doi: 10.1186/s12864-017-3800-9; GPMDB: 90.
Yimer SA, Birhanu AG, Kalayou S, Riaz T, Zegeye ED, Beyene GT, Holm-Hansen C, Norheim G, Abebe M, Aseffa A, Tønjum T, (2017) "Comparative Proteomic Analysis of Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains Reveals Differentially Abundant Proteins Linked to Slow Growth and Virulence." Front Microbiol 8:795; PMID: 28536560; doi: 10.3389/fmicb.2017.00795; GPMDB: 158.
Smallwood HS, Duan S, Morfouace M, Rezinciuc S, Shulkin BL, Shelat A, Zink EE, Milasta S, Bajracharya R, Oluwaseum AJ, Roussel MF, Green DR, Pasa-Tolic L, Thomas PG, (2017) "Targeting Metabolic Reprogramming by Influenza Infection for Therapeutic Intervention." Cell Rep 19(8):1640–1653; PMID: 28538182; doi: 10.1016/j.celrep.2017.04.039; GPMDB: 11.
Elmasri WA, Zhu R, Peng W, Al-Hariri M, Kobeissy F, Tran P, Hamood AN, Hegazy MF, Paré PW, Mechref Y, (2017) "Multitargeted Flavonoid Inhibition of the Pathogenic Bacterium Staphylococcus aureus: A Proteomic Characterization." J Proteome Res; PMID: 28541047; doi: 10.1021/acs.jproteome.7b00137; GPMDB: 12.
Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P, (2017) "eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs." Nucleic Acids Res 45(13):7997–8013; PMID: 28541577; doi: 10.1093/nar/gkx469; GPMDB: 19.
Hakimi O, Ternette N, Murphy R, Kessler BM, Carr A, (2017) "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." PLoS One 12(5):e0177656; PMID: 28542244; doi: 10.1371/journal.pone.0177656; GPMDB: 116.
Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke DM, Parker GJ, Rice RH, (2017) "Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides." Proteomics 17(13-14):; PMID: 28544375; doi: 10.1002/pmic.201600462; GPMDB: 24.
Kume K, Cantwell H, Neumann FR, Jones AW, Snijders AP, Nurse P, (2017) "A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control." PLoS Genet 13(5):e1006767; PMID: 28545058; doi: 10.1371/journal.pgen.1006767; GPMDB: 192.
Meier SM, Kreutz D, Winter L, Klose MHM, Cseh K, Weiss T, Bileck A, Alte B, Mader JC, Jana S, Chatterjee A, Bhattacharyya A, Hejl M, Jakupec MA, Heffeter P, Berger W, Hartinger CG, Keppler BK, Wiche G, Gerner C, (2017) "An Organoruthenium Anticancer Agent Shows Unexpected Target Selectivity For Plectin." Angew Chem Int Ed Engl; PMID: 28547791; doi: 10.1002/anie.201702242; GPMDB: 4.
Hou J, Li Z, Zhong W, Hao Q, Lei L, Wang L, Zhao D, Xu P, Zhou Y, Wang Y, Xu T, (2017) "Temporal Transcriptomic and Proteomic Landscapes of Deteriorating Pancreatic Islets in Type 2 Diabetic Rats." Diabetes; PMID: 28559245; doi: 10.2337/db16-1305; GPMDB: 12.
Li JY, Cai F, Ye XG, Liang JS, Li JK, Wu MY, Zhao D, Jiang ZD, You ZY, Zhong BX, (2017) "Comparative Proteomic Analysis of Posterior Silk Glands of Wild and Domesticated Silkworms Reveals Functional Evolution during Domestication." J Proteome Res 16(7):2495–2507; PMID: 28569067; doi: 10.1021/acs.jproteome.7b00077; GPMDB: 72.
Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B, (2017) "CYLD deubiquitinase is necessary for proper ubiquitination and degradation of the epidermal growth factor receptor." Mol Cell Proteomics; PMID: 28572092; doi: 10.1074/mcp.M116.066423; GPMDB: 108.
Bj Rås KØ, Sousa MML, Sharma A, Fonseca DM, S Gaard CK, Bj Rås M, Otterlei M, (2017) "Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication." Nucleic Acids Res 45(14):8291–8301; PMID: 28575236; doi: 10.1093/nar/gkx476; GPMDB: 31.
Obermann J, Priglinger CS, Merl-Pham J, Geerlof A, Priglinger S, Götz M, Hauck SM, (2017) "Proteome-wide identification of glycosylation-dependent interactors of Galectin-1 and Galectin-3 on mesenchymal retinal pigment epithelial cells." Mol Cell Proteomics; PMID: 28576849; doi: 10.1074/mcp.M116.066381; GPMDB: 193.
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) "Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function." Stem Cells; PMID: 28589555; doi: 10.1002/stem.2652; GPMDB: 36.
Zhang J, Lu S, Zhou Y, Meng K, Chen Z, Cui Y, Shi Y, Wang T, He QY, (2017) "Motile hepatocellular carcinoma cells preferentially secret sugar metabolism regulatory proteins via exosomes." Proteomics 17(13-14):; PMID: 28590090; doi: 10.1002/pmic.201700103; GPMDB: 6.
Jensen SR, Schoof EM, Wheeler SE, Hvid H, Ahnfelt-Rønne J, Hansen BF, Nishimura E, Olsen GS, Kislinger T, Brubaker PL, (2017) "Quantitative Proteomics of Intestinal Mucosa From Male Mice Lacking Intestinal Epithelial Insulin Receptors." Endocrinology 158(8):2470–2485; PMID: 28591806; doi: 10.1210/en.2017-00194; GPMDB: 10.
Pearson LJ, Klaharn IY, Thongsawang B, Manuprasert W, Saejew T, Somparn P, Chuengsaman P, Kanjanabuch T, Pisitkun T, (2017) "Multiple extracellular vesicle types in peritoneal dialysis effluent are prominent and contain known biomarkers." PLoS One 12(6):e0178601; PMID: 28594924; doi: 10.1371/journal.pone.0178601; GPMDB: 90.
Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, (2017) "An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes." Cell Syst; PMID: 28601559; doi: 10.1016/j.cels.2017.05.009; GPMDB: 93.
Haas TL, Sciuto MR, Brunetto L, Valvo C, Signore M, Fiori ME, di Martino S, Giannetti S, Morgante L, Boe A, Patrizii M, Warnken U, Schnölzer M, Ciolfi A, Di Stefano C, Biffoni M, Ricci-Vitiani L, Pallini R, De Maria R, (2017) "Integrin α7 Is a Functional Marker and Potential Therapeutic Target in Glioblastoma." Cell Stem Cell 21(1):35–50.e9; PMID: 28602620; doi: 10.1016/j.stem.2017.04.009; GPMDB: 3.
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.
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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.
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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) "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.
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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.
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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.
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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.
van den Eshof BL, Hoogendijk AJ, Simpson PJ, van Alphen FPJ, Zanivan S, Mertens K, Meijer AB, van den Biggelaar M, (2017) "Paradigm of Biased PAR1 (Protease-Activated Receptor-1) Activation and Inhibition in Endothelial Cells Dissected by Phosphoproteomics." Arterioscler Thromb Vasc Biol; PMID: 28818855; doi: 10.1161/ATVBAHA.117.309926; GPMDB: 57.
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.
Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R, (2017) "Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function." Theranostics 7(10):2704–2717; PMID: 28819457; doi: 10.7150/thno.19679; GPMDB: 663.
Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." J Proteome Res; PMID: 28823169; doi: 10.1021/acs.jproteome.7b00148; GPMDB: 14.
Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." Mol Cell Proteomics; PMID: 28827280; doi: 10.1074/mcp.RA117.000108; GPMDB: 12.
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.
Vyse S, McCarthy F, Broncel M, Paul A, Wong JP, Bhamra A, Huang PH, (2017) "Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib." J Proteomics; PMID: 28842319; doi: 10.1016/j.jprot.2017.08.015; GPMDB: 42.
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.
Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." Nature 549(7670):54–59; PMID: 28847004; doi: 10.1038/nature23482; GPMDB: 46.
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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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.
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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.
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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.
Fabrik I, Link M, Putzova D, Plzakova L, Lubovska Z, Philimonenko V, Pavkova I, Rehulka P, Krocova Z, Hozak P, Santic M, Stulik J, (2017) "The early dendritic cell signaling induced by virulent Francisellatularensis strain occurs in phases and involves the activation of ERKs and p38 in the later stage." Mol Cell Proteomics; PMID: 29046388; doi: 10.1074/mcp.RA117.000160; GPMDB: 364.
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Graham LC, Eaton SL, Brunton PJ, Atrih A, Smith C, Lamont DJ, Gillingwater TH, Pennetta G, Skehel P, Wishart TM, (2017) "Proteomic profiling of neuronal mitochondria reveals modulators of synaptic architecture." Mol Neurodegener 12(1):77; PMID: 29078798; doi: 10.1186/s13024-017-0221-9; GPMDB: 6.
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Azimi A, Caramuta S, Seashore-Ludlow B, Boström J, Robinson JL, Edfors F, Tuominen R, Kemper K, Krijgsman O, Peeper DS, Nielsen J, Hansson J, Egyhazi Brage S, Altun M, Uhlen M, Maddalo G, (2018) "Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors." Mol Syst Biol 14(3):e7858; PMID: 29507054; GPMDB: 16.
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Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN, (2018) "Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface." MBio 9(2):; PMID: 29511081; doi: 10.1128/mBio.02333-17; GPMDB: 48.
Iradi MCG, Triplett JC, Thomas JD, Davila R, Crown AM, Brown H, Lewis J, Swanson MS, Xu G, Rodriguez-Lebron E, Borchelt DR, (2018) "Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy." Sci Rep 8(1):4049; PMID: 29511296; doi: 10.1038/s41598-018-21371-4; GPMDB: 23.
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Chen JT, Liu CC, Yu JS, Li HH, Lai MC, (2018) "Integrated omics profiling identifies hypoxia-regulated genes in HCT116 colon cancer cells." J Proteomics; PMID: 29524648; doi: 10.1016/j.jprot.2018.02.031; GPMDB: 4.
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Liang P, Zhu W, Lan T, Tao Q, (2018) "Detection of salivary protein biomarkers of saliva secretion disorder in a primary Sjögren syndrome murine model." J Pharm Biomed Anal 154:252–262; PMID: 29558726; doi: 10.1016/j.jpba.2018.03.023; GPMDB: 2.
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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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Chen X, Yu C, Gao J, Zhu H, Cui B, Zhang T, Zhou Y, Liu Q, He H, Xiao R, Huang R, Xie H, Gao D, Zhou H, (2018) "A novel USP9X substrate TTK contributes to tumorigenesis in non-small-cell lung cancer." Theranostics 8(9):2348–2360; PMID: 29721084; doi: 10.7150/thno.22901; GPMDB: 1.
Zellner A, Scharrer E, Arzberger T, Oka C, Domenga-Denier V, Joutel A, Lichtenthaler SF, Müller SA, Dichgans M, Haffner C, (2018) "CADASIL brain vessels show a HTRA1 loss-of-function profile." Acta Neuropathol 136(1):111–125; PMID: 29725820; doi: 10.1007/s00401-018-1853-8; GPMDB: 12.
Van Quickelberghe E, Martens A, Goeminne LJE, Clement L, van Loo G, Gevaert K, (2018) "Identification of Immune-Responsive Gene 1 (IRG1) as a Target of A20." J Proteome Res; PMID: 29733654; doi: 10.1021/acs.jproteome.8b00139; GPMDB: 30.
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Di Lorenzo G, Voltolini Velho R, Winter D, Thelen M, Ahmadi S, Schweizer M, De Pace R, Cornils K, Yorgan TA, Grüb S, Hermans-Borgmeyer I, Schinke T, Müller-Loennies S, Braulke T, Pohl S, (2018) "Lysosomal proteome and secretome analysis identifies missorted enzymes and their non-degraded substrates in mucolipidosis III mouse cells." Mol Cell Proteomics; PMID: 29773673; doi: 10.1074/mcp.RA118.000720; GPMDB: 30.
Wang H, Cheng Q, Li X, Hu F, Han L, Zhang H, Li L, Ge J, Ying X, Guo X, Wang Q, (2018) "Loss of TIGAR induces oxidative stress and meiotic defects in oocytes from obese mice." Mol Cell Proteomics; PMID: 29776966; doi: 10.1074/mcp.RA118.000620; GPMDB: 9.
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Ternette N, Olde Nordkamp MJM, Müller J, Anderson AP, Nicastri A, Hill AVS, Kessler BM, Li D, (2018) "Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens." Proteomics 18(12):e1700465; PMID: 29786170; doi: 10.1002/pmic.201700465; GPMDB: 66.
Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, Rammensee HG, Stevanovic S, Haen SP, (2018) "Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation." Cancer Res; PMID: 29789417; doi: 10.1158/0008-5472.CAN-17-1745; GPMDB: 530.
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Nieto R LM, Mehaffy C, Islam MN, Fitzgerald B, Belisle J, Prenni J, Dobos KM, (2018) "Biochemical characterization of isoniazid resistant Mycobacterium tuberculosis: can the analysis of clonal strains reveal novel targetable pathways?" Mol Cell Proteomics; PMID: 29844232; doi: 10.1074/mcp.RA118.000821; GPMDB: 88.
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Zhou Z, Chen Y, Jin M, He J, Guli A, Yan C, Ding S, (2018) "Comprehensive analysis of lysine acetylome reveals a site-specific pattern in rapamycin-induced autophagy." J Proteome Res; PMID: 30592415; doi: 10.1021/acs.jproteome.8b00533; GPMDB: 6.
Merlos Rodrigo MA, Buchtelova H, de Los Rios V, Casal JI, Eckschlager T, Hrabeta J, Belhajova M, Heger Z, Adam V, (2019) "Proteomic Signature of Neuroblastoma Cells UKF-NB-4 Reveals Key Role of Lysosomal Sequestration and the Proteasome Complex in Acquiring Chemoresistance to Cisplatin." J Proteome Res 18(3):1255–1263; PMID: 30592607; doi: 10.1021/acs.jproteome.8b00867; GPMDB: 9.
Dunn J, Ferluga S, Sharma V, Futschik M, Hilton DA, Adams CL, Lasonder E, Hannemann OC, (2018) "Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including NEK9, HK2 and SET and deregulation of RNA metabolism." EBioMedicine; PMID: 30594554; doi: 10.1016/j.ebiom.2018.12.048; GPMDB: 78.
Żylicz JJ, Bousard A, Žumer K, Dossin F, Mohammad E, da Rocha ST, Schwalb B, Syx L, Dingli F, Loew D, Cramer P, Heard E, (2019) "The Implication of Early Chromatin Changes in X Chromosome Inactivation." Cell 176(1-2):182–197.e23; PMID: 30595450; doi: 10.1016/j.cell.2018.11.041; GPMDB: 10.
Liebelt F, Sebastian RM, Moore CL, Mulder MPC, Ovaa H, Shoulders MD, Vertegaal ACO, (2019) "SUMOylation and the HSF1-Regulated Chaperone Network Converge to Promote Proteostasis in Response to Heat Shock." Cell Rep 26(1):236–249.e4; PMID: 30605679; doi: 10.1016/j.celrep.2018.12.027; GPMDB: 57.
Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS, (2019) "Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)." Nat Biotechnol; PMID: 30607034; doi: 10.1038/s41587-018-0001-2; GPMDB: 106.
Orre LM, Vesterlund M, Pan Y, Arslan T, Zhu Y, Fernandez Woodbridge A, Frings O, Fredlund E, Lehtiö J, (2019) "SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization." Mol Cell 73(1):166–182.e7; PMID: 30609389; doi: 10.1016/j.molcel.2018.11.035; GPMDB: 18.
Landsberg CD, Megger DA, Hotter D, Rückborn MU, Eilbrecht M, Rashidi-Alavijeh J, Howe S, Heinrichs S, Sauter D, Sitek B, Le-Trilling VTK, Trilling M, (2018) "A Mass Spectrometry-Based Profiling of Interactomes of Viral DDB1- and Cullin Ubiquitin Ligase-Binding Proteins Reveals NF-κB Inhibitory Activity of the HIV-2-Encoded Vpx." Front Immunol 9:2978; PMID: 30619335; doi: 10.3389/fimmu.2018.02978; GPMDB: 48.
Yang H, Li Y, Zhao M, Wu F, Wang X, Xiao W, Wang Y, Zhang J, Wang F, Xu F, Zeng WF, Overall CM, He SM, Chi H, Xu P, (2019) "Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics." Mol Cell Proteomics; PMID: 30622160; doi: 10.1074/mcp.TIR118.000918; GPMDB: 2.
Chen D, Ludwig K, Krokhin OV, Spicer V, Yang Z, Shen X, Hummon AB, Sun L, (2019) "Capillary zone electrophoresis-tandem mass spectrometry for large-scale phosphoproteomics with the production of over 11000 phosphopeptides from the colon carcinoma HCT116 cell line." Anal Chem; PMID: 30624053; doi: 10.1021/acs.analchem.8b04770; GPMDB: 40.
Chen Z, Lei C, Wang C, Li N, Srivastava M, Tang M, Zhang H, Choi JM, Jung SY, Qin J, Chen J, (2019) "Global phosphoproteomic analysis reveals ARMC10 as an AMPK substrate that regulates mitochondrial dynamics." Nat Commun 10(1):104; PMID: 30631047; doi: 10.1038/s41467-018-08004-0; GPMDB: 30.
Hansen M, Peltier J, Killy B, Amin B, Bodendorfer B, Härtlova A, Uebel S, Bosmann M, Hofmann J, Büttner C, Ekici AB, Kuttke M, Franzyk H, Foged C, Beer-Hammer S, Schabbauer G, Trost M, Lang R, (2019) "Macrophage phosphoproteome analysis reveals MINCLE-dependent and -independent mycobacterial cord factor signaling." Mol Cell Proteomics; PMID: 30635358; doi: 10.1074/mcp.RA118.000929; GPMDB: 72.
Tripathi SK, Välikangas T, Shetty A, Khan MM, Moulder R, Bhosale SD, Komsi E, Salo V, De Albuquerque RS, Rasool O, Galande S, Elo LL, Lahesmaa R, (2019) "Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization." iScience 11:334–355; PMID: 30641411; doi: 10.1016/j.isci.2018.12.020; GPMDB: 75.
Pfaff F, Hägglund S, Zoli M, Blaise-Boisseau S, Laloy E, Koethe S, Zühlke D, Riedel K, Zientara S, Bakkali-Kassimi L, Valarcher JF, Höper D, Beer M, Eschbaumer M, (2019) "Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus." Viruses 11(1):; PMID: 30642035; doi: 10.3390/v11010053; GPMDB: 110.
Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A, (2019) "The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease." Cancer Cell 35(1):125–139.e9; PMID: 30645971; doi: 10.1016/j.ccell.2018.11.018; GPMDB: 20.
van Oorschot R, Hansen M, Koornneef JM, Marneth AE, Bergevoet SM, van Bergen MGJM, van Alphen FPJ, van der Zwaan C, Martens JHA, Vermeulen M, Jansen PWTC, Baltissen MPA, Laros-van Gorkom BAP, Janssen H, Jansen JH, von Lindern M, Meijer AB, van den Akker E, van der Reijden BA, (2019) "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets." Haematologica; PMID: 30655368; doi: 10.3324/haematol.2018.194555; GPMDB: 63.
Tsukada T, Isowa Y, Kito K, Yoshida S, Toneri S, Horiguchi K, Fujiwara K, Yashiro T, Kato T, Kato Y, (2019) "Identification of TGFβ-induced proteins in non-endocrine mouse pituitary cell line TtT/GF by SILAC-assisted quantitative mass spectrometry." Cell Tissue Res; PMID: 30666536; doi: 10.1007/s00441-018-02989-2; GPMDB: 11.
Gärtner SMK, Hundertmark T, Nolte H, Theofel I, Eren-Ghiani Z, Tetzner C, Duchow TB, Rathke C, Krüger M, Renkawitz-Pohl R, (2019) "Stage-specific testes proteomics of Drosophila melanogaster identifies essential proteins for male fertility." Eur J Cell Biol; PMID: 30679029; doi: 10.1016/j.ejcb.2019.01.001; GPMDB: 180.
Fornecker LM, Muller L, Bertrand F, Paul N, Pichot A, Herbrecht R, Chenard MP, Mauvieux L, Vallat L, Bahram S, Cianférani S, Carapito R, Carapito C, (2019) "Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma." Sci Rep 9(1):895; PMID: 30696890; doi: 10.1038/s41598-018-37273-4; GPMDB: 20.
McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ, (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." J Proteome Res; PMID: 30735395; doi: 10.1021/acs.jproteome.9b00004; GPMDB: 22.
Furuyama K, Chera S, van Gurp L, Oropeza D, Ghila L, Damond N, Vethe H, Paulo JA, Joosten AM, Berney T, Bosco D, Dorrell C, Grompe M, Ræder H, Roep BO, Thorel F, Herrera PL, (2019) "Diabetes relief in mice by glucose-sensing insulin-secreting human α-cells." Nature 567(7746):43–48; PMID: 30760930; doi: 10.1038/s41586-019-0942-8; GPMDB: 1.
Mohanty V, Subbannayya Y, Najar MA, Pinto SM, Kasaragod S, Karuppiah H, Sreeramulu B, Singh KK, Dalal S, Manikkoth S, Arunachalam C, Prasad TSK, Murthy KR, (2019) "Proteomics and Visual Health Research: Proteome of the Human Sclera Using High-Resolution Mass Spectrometry." OMICS 23(2):98–110; PMID: 30767726; doi: 10.1089/omi.2018.0185; GPMDB: 2.
Patil S, Subbannayya T, Mohan SV, Babu N, Advani J, Sathe G, Rajagopalan P, Patel K, Bhandi S, Solanki H, Sidransky D, Gowda H, Chatterjee A, Ferrari M, (2019) "Proteomic Changes in Oral Keratinocytes Chronically Exposed to Shisha (Water Pipe)." OMICS 23(2):86–97; PMID: 30767727; doi: 10.1089/omi.2018.0173; GPMDB: 18.
Eraslan B, Wang D, Gusic M, Prokisch H, Hallström BM, Uhlén M, Asplund A, Pontén F, Wieland T, Hopf T, Hahne H, Kuster B, Gagneur J, (2019) "Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues." Mol Syst Biol 15(2):e8513; PMID: 30777893; doi: 10.15252/msb.20188513; GPMDB: 28.
Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E, (2019) "Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation." Mol Cell Proteomics; PMID: 30808727; doi: 10.1074/mcp.RA119.001316; GPMDB: 20.
Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, Tsitsiridis G, Ansari M, Graf E, Strom TM, Nagendran M, Desai T, Eickelberg O, Mann M, Theis FJ, Schiller HB, (2019) "An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics." Nat Commun 10(1):963; PMID: 30814501; doi: 10.1038/s41467-019-08831-9; GPMDB: 32.
Parker BL, Calkin AC, Seldin MM, Keating MF, Tarling EJ, Yang P, Moody SC, Liu Y, Zerenturk EJ, Needham EJ, Miller ML, Clifford BL, Morand P, Watt MJ, Meex RCR, Peng KY, Lee R, Jayawardana K, Pan C, Mellett NA, Weir JM, Lazarus R, Lusis AJ, Meikle PJ, James DE, de Aguiar Vallim TQ, Drew BG, (2019) "An integrative systems genetic analysis of mammalian lipid metabolism." Nature 567(7747):187–193; PMID: 30814737; doi: 10.1038/s41586-019-0984-y; GPMDB: 78.
Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, Xing B, Sun W, Ren L, Hu B, Li C, Zhang L, Qin G, Zhang M, Chen N, Zhang M, Huang Y, Zhou J, Zhao Y, Liu M, Zhu X, Qiu Y, Sun Y, Huang C, Yan M, Wang M, Liu W, Tian F, Xu H, Zhou J, Wu Z, Shi T, Zhu W, Qin J, Xie L, Fan J, Qian X, He F, Chinese Human Proteome Project (CNHPP) Consortium., (2019) "Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma." Nature 567(7747):257–261; PMID: 30814741; doi: 10.1038/s41586-019-0987-8; GPMDB: 688.
Brummer T, Müller SA, Pan-Montojo F, Yoshida F, Fellgiebel A, Tomita T, Endres K, Lichtenthaler SF, (2019) "NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer's disease." EMBO Mol Med 11(4):; PMID: 30833305; doi: 10.15252/emmm.201809695; GPMDB: 72.
Hansen BK, Gupta R, Baldus L, Lyon D, Narita T, Lammers M, Choudhary C, Weinert BT, (2019) "Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation." Nat Commun 10(1):1055; PMID: 30837475; doi: 10.1038/s41467-019-09024-0; GPMDB: 123.
Marei WFA, Van Raemdonck G, Baggerman G, Bols PEJ, Leroy JLMR, (2019) "Proteomic changes in oocytes after in vitro maturation in lipotoxic conditions are different from those in cumulus cells." Sci Rep 9(1):3673; PMID: 30842615; doi: 10.1038/s41598-019-40122-7; GPMDB: 2.
Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y, (2019) "Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery." J Proteome Res; PMID: 30848925; doi: 10.1021/acs.jproteome.9b00037; GPMDB: 51.
Herbst FA, Gonçalves SCL, Behr T, McIlroy SJ, Nielsen PH, (2019) "Proteogenomic Refinement of the Neomegalonema perideroedes^T Genome Annotation." Proteomics :e1800330; PMID: 30865376; doi: 10.1002/pmic.201800330; GPMDB: 9.
Gallud A, Klöditz K, Ytterberg J, Östberg N, Katayama S, Skoog T, Gogvadze V, Chen YZ, Xue D, Moya S, Ruiz J, Astruc D, Zubarev R, Kere J, Fadeel B, (2019) "Cationic gold nanoparticles elicit mitochondrial dysfunction: a multi-omics study." Sci Rep 9(1):4366; PMID: 30867451; doi: 10.1038/s41598-019-40579-6; GPMDB: 45.
Obradović MMS, Hamelin B, Manevski N, Couto JP, Sethi A, Coissieux MM, Münst S, Okamoto R, Kohler H, Schmidt A, Bentires-Alj M, (2019) "Glucocorticoids promote breast cancer metastasis." Nature 567(7749):540–544; PMID: 30867597; doi: 10.1038/s41586-019-1019-4; GPMDB: 23.
Berg P, McConnell EW, Hicks LM, Popescu SC, Popescu GV, (2019) "Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics." BMC Bioinformatics 20(Suppl 2):102; PMID: 30871482; doi: 10.1186/s12859-019-2619-6; GPMDB: 1.
Vandervore LV, Schot R, Kasteleijn E, Oegema R, Stouffs K, Gheldof A, Grochowska MM, van der Sterre MLT, van Unen LMA, Wilke M, Elfferich P, van der Spek PJ, Heijsman D, Grandone A, Demmers JAA, Dekkers DHW, Slotman JA, Kremers GJ, Schaaf GJ, Masius RG, van Essen AJ, Rump P, van Haeringen A, Peeters E, Altunoglu U, Kalayci T, Poot RA, Dobyns WB, Bahi-Buisson N, Verheijen FW, Jansen AC, Mancini GMS, (2019) "Heterogeneous clinical phenotypes and cerebral malformations reflected by rotatin cellular dynamics." Brain; PMID: 30879067; doi: 10.1093/brain/awz045; GPMDB: 14.
Sacco F, Seelig A, Humphrey SJ, Krahmer N, Volta F, Reggio A, Marchetti P, Gerdes J, Mann M, (2019) "Phosphoproteomics Reveals the GSK3-PDX1 Axis as a Key Pathogenic Signaling Node in Diabetic Islets." Cell Metab; PMID: 30879985; doi: 10.1016/j.cmet.2019.02.012; GPMDB: 24.
Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC, (2019) "The Proteogenomic Landscape of Curable Prostate Cancer." Cancer Cell 35(3):414–427.e6; PMID: 30889379; doi: 10.1016/j.ccell.2019.02.005; GPMDB: 108.
Xu B, Zheng C, Chen X, Zhang Z, Liu J, Spencer P, Yang X, (2019) "Dysregulation of Myosin Complex and Striated Muscle Contraction Pathway in the Brain of ALS-SOD1 mouse model." ACS Chem Neurosci; PMID: 30889949; doi: 10.1021/acschemneuro.8b00704; GPMDB: 1.
Borgermann N, Ackermann L, Schwertman P, Hendriks IA, Thijssen K, Liu JC, Lans H, Nielsen ML, Mailand N, (2019) "SUMOylation promotes protective responses to DNA-protein crosslinks." EMBO J; PMID: 30914427; doi: 10.15252/embj.2019101496; GPMDB: 52.
Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G, (2019) "Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data." Sci Rep 9(1):5154; PMID: 30914758; doi: 10.1038/s41598-019-41625-z; GPMDB: 111.
Sinclair LV, Howden AJ, Brenes A, Spinelli L, Hukelmann JL, Macintyre AN, Liu X, Thomson S, Taylor PM, Rathmell JC, Locasale JW, Lamond AI, Cantrell DA, (2019) "Antigen receptor control of methionine metabolism in T cells." Elife; PMID: 30916644; doi: 10.7554/eLife.44210; GPMDB: 7.
Chachami G, Stankovic-Valentin N, Karagiota A, Basagianni A, Plessmann U, Urlaub H, Melchior F, Simos G, (2019) "Hypoxia-induced changes in SUMO conjugation affect transcriptional regulation under low oxygen." Mol Cell Proteomics; PMID: 30926672; doi: 10.1074/mcp.RA119.001401; GPMDB: 69.
Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T, (2019) "Proteomics profiling of arginine methylation defines PRMT5 substrate specificity." Sci Signal 12(575):; PMID: 30940768; doi: 10.1126/scisignal.aat8388; GPMDB: 76.
Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K, (2019) "Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia." Nat Commun 10(1):1519; PMID: 30944321; doi: 10.1038/s41467-019-09469-3; GPMDB: 3.
Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B, Consortia Oslo Breast Cancer Research Consortium (OSBREAC)., Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale AL, Lehtiö J, (2019) "Breast cancer quantitative proteome and proteogenomic landscape." Nat Commun 10(1):1600; PMID: 30962452; doi: 10.1038/s41467-019-09018-y; GPMDB: 12.
Erhart F, Weiss T, Klingenbrunner S, Fischhuber K, Reitermaier R, Halfmann A, Blauensteiner B, Lötsch D, Spiegl-Kreinecker S, Berger W, Sialana FJ, Lubec G, Felzmann T, Dohnal A, Visus C, (2019) "Spheroid glioblastoma culture conditions as antigen source for dendritic cell-based immunotherapy: spheroid proteins are survival-relevant targets but can impair immunogenic interferon γ production." Cytotherapy; PMID: 30975602; doi: 10.1016/j.jcyt.2019.03.002; GPMDB: 8.
Na CH, Sharma N, Madugundu AK, Chen R, Atalar Aksit M, Rosson GD, Cutting GR, Pandey A, (2019) "Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins." Mol Cell Proteomics; PMID: 30979791; doi: 10.1074/mcp.RA118.001101; GPMDB: 3.
Guergues J, Zhang P, Liu B, Stevens SM Jr, (2019) "Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult-Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model." Proteomics :e1800469; PMID: 30980500; doi: 10.1002/pmic.201800469; GPMDB: 6.
Zhou B, Yan Y, Wang Y, You S, Freeman MR, Yang W, (2019) "Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer." Clin Proteomics 16:15; PMID: 31011308; doi: 10.1186/s12014-019-9236-2; GPMDB: 2.
Trzeciecka A, Bhattacharya SK, (2019) "Dataset of growth cone-enriched lipidome and proteome of embryonic to early postnatal mouse brain." Data Brief 24:103865; PMID: 31016214; doi: 10.1016/j.dib.2019.103865; GPMDB: 60.
Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, Königsrainer I, Thiel K, Nadalin S, Beckert S, Bösmüller H, Fend F, Velic A, Maček B, Haen SP, Buonaguro L, Kohlbacher O, Stevanović S, Königsrainer A, HEPAVAC Consortium., Rammensee HG, (2019) "Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma." Genome Med 11(1):28; PMID: 31039795; doi: 10.1186/s13073-019-0636-8; GPMDB: 178.

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

@@ Line 27: / Line 27: @@
 ==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 May 5, 2019.
+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 May 12, 2019.
 #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].
@@ Line 1,997: / Line 1,997: @@
 #Parker BL, Calkin AC, Seldin MM, Keating MF, Tarling EJ, Yang P, Moody SC, Liu Y, Zerenturk EJ, Needham EJ, Miller ML, Clifford BL, Morand P, Watt MJ, Meex RCR, Peng KY, Lee R, Jayawardana K, Pan C, Mellett NA, Weir JM, Lazarus R, Lusis AJ, Meikle PJ, James DE, de Aguiar Vallim TQ, Drew BG,  (2019) &quot;An integrative systems genetic analysis of mammalian lipid metabolism.&quot; <i>Nature</i> <b>567</b>(7747):187&ndash;193; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814737 30814737]; doi: [https://dx.doi.org/10.1038/s41586-019-0984-y 10.1038/s41586-019-0984-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814737 78].
 #Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, Xing B, Sun W, Ren L, Hu B, Li C, Zhang L, Qin G, Zhang M, Chen N, Zhang M, Huang Y, Zhou J, Zhao Y, Liu M, Zhu X, Qiu Y, Sun Y, Huang C, Yan M, Wang M, Liu W, Tian F, Xu H, Zhou J, Wu Z, Shi T, Zhu W, Qin J, Xie L, Fan J, Qian X, He F, Chinese Human Proteome Project (CNHPP) Consortium.,  (2019) &quot;Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma.&quot; <i>Nature</i> <b>567</b>(7747):257&ndash;261; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814741 30814741]; doi: [https://dx.doi.org/10.1038/s41586-019-0987-8 10.1038/s41586-019-0987-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814741 688].
-#Brummer T, M&uuml;ller SA, Pan-Montojo F, Yoshida F, Fellgiebel A, Tomita T, Endres K, Lichtenthaler SF,  (2019) &quot;NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer&#39;s disease.&quot; <i>EMBO Mol Med</i> <b>11</b>(4):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30833305 30833305]; doi: [https://dx.doi.org/10.15252/emmm.201809695 10.15252/emmm.201809695]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30833305 36].
+#Brummer T, M&uuml;ller SA, Pan-Montojo F, Yoshida F, Fellgiebel A, Tomita T, Endres K, Lichtenthaler SF,  (2019) &quot;NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer&#39;s disease.&quot; <i>EMBO Mol Med</i> <b>11</b>(4):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30833305 30833305]; doi: [https://dx.doi.org/10.15252/emmm.201809695 10.15252/emmm.201809695]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30833305 72].
 #Hansen BK, Gupta R, Baldus L, Lyon D, Narita T, Lammers M, Choudhary C, Weinert BT,  (2019) &quot;Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation.&quot; <i>Nat Commun</i> <b>10</b>(1):1055; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30837475 30837475]; doi: [https://dx.doi.org/10.1038/s41467-019-09024-0 10.1038/s41467-019-09024-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30837475 123].
 #Marei WFA, Van Raemdonck G, Baggerman G, Bols PEJ, Leroy JLMR,  (2019) &quot;Proteomic changes in oocytes after in vitro maturation in lipotoxic conditions are different from those in cumulus cells.&quot; <i>Sci Rep</i> <b>9</b>(1):3673; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30842615 30842615]; doi: [https://dx.doi.org/10.1038/s41598-019-40122-7 10.1038/s41598-019-40122-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30842615 2].
@@ Line 2,019: / Line 2,019: @@
 #Na CH, Sharma N, Madugundu AK, Chen R, Atalar Aksit M, Rosson GD, Cutting GR, Pandey A,  (2019) &quot;Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins.&quot; <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30979791 30979791]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001101 10.1074/mcp.RA118.001101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30979791 3].
 #Guergues J, Zhang P, Liu B, Stevens SM Jr,  (2019) &quot;Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult-Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model.&quot; <i>Proteomics</i> <b></b>:e1800469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30980500 30980500]; doi: [https://dx.doi.org/10.1002/pmic.201800469 10.1002/pmic.201800469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30980500 6].
-#Zhou B, Yan Y, Wang Y, You S, Freeman MR, Yang W,  (2019) &quot;Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer.&quot; <i>Clin Proteomics</i> <b>16</b>:15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31011308 31011308]; doi: [https://dx.doi.org/10.1186/s12014-019-9236-2 10.1186/s12014-019-9236-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31011308 1].
+#Zhou B, Yan Y, Wang Y, You S, Freeman MR, Yang W,  (2019) &quot;Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer.&quot; <i>Clin Proteomics</i> <b>16</b>:15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31011308 31011308]; doi: [https://dx.doi.org/10.1186/s12014-019-9236-2 10.1186/s12014-019-9236-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31011308 2].
+#Trzeciecka A, Bhattacharya SK,  (2019) &quot;Dataset of growth cone-enriched lipidome and proteome of embryonic to early postnatal mouse brain.&quot; <i>Data Brief</i> <b>24</b>:103865; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31016214 31016214]; doi: [https://dx.doi.org/10.1016/j.dib.2019.103865 10.1016/j.dib.2019.103865]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31016214 60].
+#L&ouml;ffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, M&uuml;hlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, K&ouml;nigsrainer I, Thiel K, Nadalin S, Beckert S, B&ouml;sm&uuml;ller H, Fend F, Velic A, Ma&#x10D;ek B, Haen SP, Buonaguro L, Kohlbacher O, Stevanovi&#x107; S, K&ouml;nigsrainer A, HEPAVAC Consortium., Rammensee HG,  (2019) &quot;Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma.&quot; <i>Genome Med</i> <b>11</b>(1):28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31039795 31039795]; doi: [https://dx.doi.org/10.1186/s13073-019-0636-8 10.1186/s13073-019-0636-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31039795 178].

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