GPMDB Data Sources

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Revision as of 19:14, 6 January 2022

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Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.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 Jan 2, 2022.

Lipton MS, et al. (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, et al. (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, et al. (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, et al. (2005) "The membrane proteome of Halobacterium salinarum." Proteomics 5(1):180–97; PMID: 15619294; doi: 10.1002/pmic.200400943; GPMDB: 37.
Searle BC, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (2007) "Genome-wide proteomics of Natronomonas pharaonis." J Proteome Res 6(1):185–93; PMID: 17203963; doi: 10.1021/pr060352q; GPMDB: 176.
Villén J, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (2008) "Phosphoproteome analysis of Drosophila melanogaster embryos." J Proteome Res 7(4):1675–82; PMID: 18327897; doi: 10.1021/pr700696a; GPMDB: 24.
Denny P, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (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, et al. (2008) "Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry." J Proteome Res 7(12):5314–26; PMID: 19367708; doi: 10.1021/pr800599n; GPMDB: 20.
Reiland S, et al. (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, et al. (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, et al. (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, et al. (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, et al. (2009) "Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis." Mol Cell Proteomics 8(8):1988–98; PMID: 19467989; doi: 10.1074/mcp.M800518-MCP200; GPMDB: 230.
Burkard ME, et al. (2009) "Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells." PLoS Biol 7(5):e1000111; PMID: 19468302; doi: 10.1371/journal.pbio.1000111; GPMDB: 1.
Samaee SM, et al. (2009) "Quantitative composition of vitellogenin-derived yolk proteins and their effects on viability of embryos and larvae of common dentex (Dentex dentex), a marine pelagophil teleost." J Exp Zool A Ecol Genet Physiol 311(7):504–20; PMID: 19492308; doi: 10.1002/jez.548; GPMDB: 4.
Ma ZQ, et al. (2009) "IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering." J Proteome Res 8(8):3872–81; PMID: 19522537; doi: 10.1021/pr900360j; GPMDB: 18.
Shi L, et al. (2009) "Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica." Infect Immun 77(8):3227–33; PMID: 19528222; doi: 10.1128/IAI.00063-09; GPMDB: 29.
Cox B, et al. (2009) "Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology." Mol Syst Biol 5:279; PMID: 19536202; doi: 10.1038/msb.2009.37; GPMDB: 166.
Kentsis A, et al. (2010) "Discovery and validation of urine markers of acute pediatric appendicitis using high-accuracy mass spectrometry." Ann Emerg Med 55(1):62–70.e4; PMID: 19556024; doi: 10.1016/j.annemergmed.2009.04.020; GPMDB: 311.
Lau NC, et al. (2009) "Human Ccr4-Not complexes contain variable deadenylase subunits." Biochem J 422(3):443–53; PMID: 19558367; doi: 10.1042/BJ20090500; GPMDB: 10.
Zivanovic Y, et al. (2009) "Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea." Genome Biol 10(6):R70; PMID: 19558674; doi: 10.1186/gb-2009-10-6-r70; GPMDB: 7.
Alev C, et al. (2009) "Genomic organization of zebra finch alpha and beta globin genes and their expression in primitive and definitive blood in comparison with globins in chicken." Dev Genes Evol 219(7):353–60; PMID: 19609557; doi: 10.1007/s00427-009-0294-8; GPMDB: 8.
Izquierdo L, et al. (2009) "Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases." EMBO J 28(17):2650–61; PMID: 19629045; doi: 10.1038/emboj.2009.203; GPMDB: 1.
Van Hoof D, et al. (2009) "Phosphorylation dynamics during early differentiation of human embryonic stem cells." Cell Stem Cell 5(2):214–26; PMID: 19664995; doi: 10.1016/j.stem.2009.05.021; GPMDB: 12.
Tebbe A, et al. (2009) "Life-style changes of a halophilic archaeon analyzed by quantitative proteomics." Proteomics 9(15):3843–55; PMID: 19670246; doi: 10.1002/pmic.200800944; GPMDB: 43.
Casado-Vela J, et al. (2009) "Comprehensive proteomic analysis of human endometrial fluid aspirate." J Proteome Res 8(10):4622–32; PMID: 19670903; doi: 10.1021/pr9004426; GPMDB: 4.
Charles RC, et al. (2009) "Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium." PLoS One 4(9):e6994; PMID: 19746165; doi: 10.1371/journal.pone.0006994; GPMDB: 6.
Pottiez G, et al. (2009) "Understanding the blood-brain barrier using gene and protein expression profiling technologies." Brain Res Rev 62(1):83–98; PMID: 19770003; doi: 10.1016/j.brainresrev.2009.09.004; GPMDB: 6.
Boersema PJ, et al. (2010) "In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling." Mol Cell Proteomics 9(1):84–99; PMID: 19770167; doi: 10.1074/mcp.M900291-MCP200; GPMDB: 4.
Ozlü N, et al. (2010) "Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition." Mol Cell Proteomics 9(2):336–50; PMID: 19786723; doi: 10.1074/mcp.M900308-MCP200; GPMDB: 13.
Johansen E, et al. (2009) "A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples." J Vis Exp (32):; PMID: 19798022; doi: 10.3791/1398; GPMDB: 83.
Hahn CK, et al. (2009) "Proteomic and genetic approaches identify Syk as an AML target." Cancer Cell 16(4):281–94; PMID: 19800574; doi: 10.1016/j.ccr.2009.08.018; GPMDB: 8.
Delmotte N, et al. (2009) "Community proteogenomics reveals insights into the physiology of phyllosphere bacteria." Proc Natl Acad Sci U S A 106(38):16428–33; PMID: 19805315; doi: 10.1073/pnas.0905240106; GPMDB: 11.
Tunica DG, et al. (2009) "Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS." Proteomics 9(21):4991–6; PMID: 19810032; doi: 10.1002/pmic.200900065; GPMDB: 1.
Mathivanan S, et al. (2010) "Proteomics analysis of A33 immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature." Mol Cell Proteomics 9(2):197–208; PMID: 19837982; doi: 10.1074/mcp.M900152-MCP200; GPMDB: 84.
Baudet M, et al. (2010) "Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons." Mol Cell Proteomics 9(2):415–26; PMID: 19875382; doi: 10.1074/mcp.M900359-MCP200; GPMDB: 19.
Pitteri SJ, et al. (2009) "Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery." PLoS One 4(11):e7916; PMID: 19936259; doi: 10.1371/journal.pone.0007916; GPMDB: 144.
Bilodeau N, et al. (2010) "Proteomic analysis of Src family kinases signaling complexes in Golgi/endosomal fractions using a site-selective anti-phosphotyrosine antibody: identification of LRP1-insulin receptor complexes." J Proteome Res 9(2):708–17; PMID: 19947650; doi: 10.1021/pr900481b; GPMDB: 17.
Mathias RA, et al. (2010) "Extracellular remodelling during oncogenic Ras-induced epithelial-mesenchymal transition facilitates MDCK cell migration." J Proteome Res 9(2):1007–19; PMID: 19954229; doi: 10.1021/pr900907g; GPMDB: 66.
Lau TY, et al. (2010) "Prioritization of candidate protein biomarkers from an in vitro model system of breast tumor progression toward clinical verification." J Proteome Res 9(3):1450–9; PMID: 20000743; doi: 10.1021/pr900989q; GPMDB: 5.
Chalkley RJ, et al. (2010) "Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry." Anal Chem 82(2):579–84; PMID: 20028093; doi: 10.1021/ac9018582; GPMDB: 2.
Yin X, et al. (2010) "Proteomics analysis of the cardiac myofilament subproteome reveals dynamic alterations in phosphatase subunit distribution." Mol Cell Proteomics 9(3):497–509; PMID: 20037178; doi: 10.1074/mcp.M900275-MCP200; GPMDB: 156.
Friso G, et al. (2010) "Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly." Plant Physiol 152(3):1219–50; PMID: 20089766; doi: 10.1104/pp.109.152694; GPMDB: 301.
Gant-Branum RL, et al. (2010) "Identification of phosphorylation sites within the signaling adaptor APPL1 by mass spectrometry." J Proteome Res 9(3):1541–8; PMID: 20095645; doi: 10.1021/pr901043e; GPMDB: 8.
Paweletz CP, et al. (2010) "Application of an end-to-end biomarker discovery platform to identify target engagement markers in cerebrospinal fluid by high resolution differential mass spectrometry." J Proteome Res 9(3):1392–401; PMID: 20095649; doi: 10.1021/pr900925d; GPMDB: 144.
Guo X, et al. (2010) "Proteomic analysis of proteins involved in spermiogenesis in mouse." J Proteome Res 9(3):1246–56; PMID: 20099899; doi: 10.1021/pr900735k; GPMDB: 1.
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Friedrich C, et al. (2021) "Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories." Nat Commun 12(1):3576; PMID: 34117251; doi: 10.1038/s41467-021-23855-w; GPMDB: 154.
Mercer TJ, et al. (2021) "Phosphoproteomic identification of ULK substrates reveals VPS15-dependent ULK/VPS34 interplay in the regulation of autophagy." EMBO J 40(14):e105985; PMID: 34121209; doi: 10.15252/embj.2020105985; GPMDB: 234.
de la Calle Arregui C, et al. (2021) "Limited survival and impaired hepatic fasting metabolism in mice with constitutive Rag GTPase signaling." Nat Commun 12(1):3660; PMID: 34135321; doi: 10.1038/s41467-021-23857-8; GPMDB: 3.
Zeng X, et al. (2021) "MSTracer: A Machine Learning Software Tool for Peptide Feature Detection from Liquid Chromatography-Mass Spectrometry Data." J Proteome Res 20(7):3455–3462; PMID: 34137255; doi: 10.1021/acs.jproteome.0c01029; GPMDB: 3.
Griffante G, et al. (2021) "Human cytomegalovirus-induced host protein citrullination is crucial for viral replication." Nat Commun 12(1):3910; PMID: 34162877; doi: 10.1038/s41467-021-24178-6; GPMDB: 15.
Nagler A, et al. (2021) "Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics." Cell Rep 35(13):109305; PMID: 34166618; doi: 10.1016/j.celrep.2021.109305; GPMDB: 144.
Brauer M, et al. (2021) "What's a Biofilm?-How the Choice of the Biofilm Model Impacts the Protein Inventory of Clostridioides difficile." Front Microbiol 12:682111; PMID: 34177868; doi: 10.3389/fmicb.2021.682111; GPMDB: 240.
Hirama T, et al. (2021) "Proteogenomic identification of an immunogenic HLA class I neoantigen in mismatch repair-deficient colorectal cancer tissue." JCI Insight 6(14):; PMID: 34185709; doi: 10.1172/jci.insight.146356; GPMDB: 11.
Schaffert A, et al. (2021) "Alternatives for the worse: Molecular insights into adverse effects of bisphenol a and substitutes during human adipocyte differentiation." Environ Int 156:106730; PMID: 34186270; doi: 10.1016/j.envint.2021.106730; GPMDB: 169.
Schlagowski AM, et al. (2021) "Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol." EMBO J 40(16):e107913; PMID: 34191328; doi: 10.15252/embj.2021107913; GPMDB: 3.
Vaz C, et al. (2021) "Mass Spectrometry-Based Proteomic and Immunoproteomic Analyses of the Candida albicans Hyphal Secretome Reveal Diagnostic Biomarker Candidates for Invasive Candidiasis." J Fungi (Basel) 7(7):; PMID: 34201883; doi: 10.3390/jof7070501; GPMDB: 2.
Rusanov AL, et al. (2021) "Proteome Profiling of PMJ2-R and Primary Peritoneal Macrophages." Int J Mol Sci 22(12):; PMID: 34204832; doi: 10.3390/ijms22126323; GPMDB: 18.
Bauzá-Martinez J, et al. (2021) "HLA-B and cysteinylated ligands distinguish the antigen presentation landscape of extracellular vesicles." Commun Biol 4(1):825; PMID: 34211107; doi: 10.1038/s42003-021-02364-y; GPMDB: 12.
Yang H, et al. (2021) "Heat Adaptation Induced Cross Protection Against Ethanol Stress in Tetragenococcus halophilus: Physiological Characteristics and Proteomic Analysis." Front Microbiol 12:686672; PMID: 34220775; doi: 10.3389/fmicb.2021.686672; GPMDB: 14.
Stingl C, et al. (2021) "Alteration of protein expression and spliceosome pathway activity during Barrett's carcinogenesis." J Gastroenterol 56(9):791–807; PMID: 34227026; doi: 10.1007/s00535-021-01802-2; GPMDB: 91.
Wu Q, et al. (2021) "Large-Scale Proteomic Assessment of Urinary Extracellular Vesicles Highlights Their Reliability in Reflecting Protein Changes in the Kidney." J Am Soc Nephrol 32(9):2195–2209; PMID: 34230103; doi: 10.1681/ASN.2020071035; GPMDB: 34.
Chen DY, et al. (2021) "SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway." J Virol 95(19):e0086221; PMID: 34260266; doi: 10.1128/JVI.00862-21; GPMDB: 6.
Adam RJ, et al. (2020) "Functionally Essential Tubular Proteins Are Lost to Urine-Excreted, Large Extracellular Vesicles during Chronic Renal Insufficiency." Kidney360 1(10):1105–1115; PMID: 34263177; doi: 10.34067/kid.0001212020; GPMDB: 9.
Israel S, et al. (2021) "The COP9 signalosome subunit 3 is necessary for early embryo survival by way of a stable protein deposit in mouse oocytes." Mol Hum Reprod 27(8):; PMID: 34264319; doi: 10.1093/molehr/gaab048; GPMDB: 130.
Kesavan R, et al. (2021) "The Consequences of Soluble Epoxide Hydrolase Deletion on Tumorigenesis and Metastasis in a Mouse Model of Breast Cancer." Int J Mol Sci 22(13):; PMID: 34281173; doi: 10.3390/ijms22137120; GPMDB: 13.
de Azambuja Rodrigues PM, et al. (2021) "Proteomics reveals disturbances in the immune response and energy metabolism of monocytes from patients with septic shock." Sci Rep 11(1):15149; PMID: 34312428; doi: 10.1038/s41598-021-94474-0; GPMDB: 72.
Striednig B, et al. (2021) "Quorum sensing governs a transmissive Legionella subpopulation at the pathogen vacuole periphery." EMBO Rep 22(9):e52972; PMID: 34314090; doi: 10.15252/embr.202152972; GPMDB: 8.
Tabang DN, et al. (2021) "Analysis of pancreatic extracellular matrix protein post-translational modifications via electrostatic repulsion-hydrophilic interaction chromatography coupled with mass spectrometry." Mol Omics 17(5):652–664; PMID: 34318855; doi: 10.1039/d1mo00104c; GPMDB: 64.
Koyuncu S, et al. (2021) "Rewiring of the ubiquitinated proteome determines ageing in C. elegans." Nature 596(7871):285–290; PMID: 34321666; doi: 10.1038/s41586-021-03781-z; GPMDB: 72.
Psakhye I, et al. (2021) "SMC complexes are guarded by the SUMO protease Ulp2 against SUMO-chain-mediated turnover." Cell Rep 36(5):109485; PMID: 34348159; doi: 10.1016/j.celrep.2021.109485; GPMDB: 2.
Vanderboom PM, et al. (2021) "A size-exclusion-based approach for purifying extracellular vesicles from human plasma." Cell Rep Methods 1(3):; PMID: 34355211; doi: 10.1016/j.crmeth.2021.100055; GPMDB: 140.
Jang HN, et al. (2021) "Mass Spectrometry-Based Proteomic Discovery of Prognostic Biomarkers in Adrenal Cortical Carcinoma." Cancers (Basel) 13(15):; PMID: 34359790; doi: 10.3390/cancers13153890; GPMDB: 174.
Wang HZ, et al. (2021) "Cerebrospinal fluid proteomics reveal potential protein targets of JiaWeiSiNiSan in preventing chronic psychological stress damage." Pharm Biol 59(1):1065–1076; PMID: 34383630; doi: 10.1080/13880209.2021.1954666; GPMDB: 3.
Qi YA, et al. (2021) "Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma." Mol Cell Proteomics 20:100136; PMID: 34391887; doi: 10.1016/j.mcpro.2021.100136; GPMDB: 27.
Klaeger S, et al. (2021) "Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples." Mol Cell Proteomics 20:100133; PMID: 34391888; doi: 10.1016/j.mcpro.2021.100133; GPMDB: 230.
ElAbd H, et al. (2021) "Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data." BMC Bioinformatics 22(1):405; PMID: 34404349; doi: 10.1186/s12859-021-04315-0; GPMDB: 4.
Aviner R, et al. (2021) "Cotranslational prolyl hydroxylation is essential for flavivirus biogenesis." Nature 596(7873):558–564; PMID: 34408324; doi: 10.1038/s41586-021-03851-2; GPMDB: 63.
Kikuchi Y, et al. (2021) "CD8⁺ T-cell Immune Surveillance against a Tumor Antigen Encoded by the Oncogenic Long Noncoding RNA PVT1." Cancer Immunol Res 9(11):1342–1353; PMID: 34433589; doi: 10.1158/2326-6066.CIR-20-0964; GPMDB: 11.
Gonzalez-Franquesa A, et al. (2021) "Insulin and 5-Aminoimidazole-4-Carboxamide Ribonucleotide (AICAR) Differentially Regulate the Skeletal Muscle Cell Secretome." Proteomes 9(3):; PMID: 34449730; doi: 10.3390/proteomes9030037; GPMDB: 34.
Sripathi SR, et al. (2021) "Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT." Mol Cell Proteomics 20:100131; PMID: 34455105; doi: 10.1016/j.mcpro.2021.100131; GPMDB: 2.
Carruthers NJ, et al. (2021) "The human type 2 diabetes-specific visceral adipose tissue proteome and transcriptome in obesity." Sci Rep 11(1):17394; PMID: 34462518; doi: 10.1038/s41598-021-96995-0; GPMDB: 20.
Wang H, et al. (2021) "An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism." Mol Cell Proteomics 20:100141; PMID: 34478876; doi: 10.1016/j.mcpro.2021.100141; GPMDB: 6.
Frankovsky J, et al. (2021) "The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids." J Biol Chem 297(4):101155; PMID: 34480900; doi: 10.1016/j.jbc.2021.101155; GPMDB: 36.
Mukherjee S, et al. (2021) "Citrullination of Amyloid-β Peptides in Alzheimer's Disease." ACS Chem Neurosci 12(19):3719–3732; PMID: 34519476; doi: 10.1021/acschemneuro.1c00474; GPMDB: 10.
Zhang X, et al. (2021) "The Insufficient Activation of RIG-I-Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells." Mol Cell Proteomics 20:100147; PMID: 34530158; doi: 10.1016/j.mcpro.2021.100147; GPMDB: 4.
Tognoli ML, et al. (2021) "RASSF1C oncogene elicits amoeboid invasion, cancer stemness, and extracellular vesicle release via a SRC/Rho axis." EMBO J 40(20):e107680; PMID: 34532864; doi: 10.15252/embj.2021107680; GPMDB: 4.
Champagne J, et al. (2021) "Oncogene-dependent sloppiness in mRNA translation." Mol Cell 81(22):4709–4721.e9; PMID: 34562372; doi: 10.1016/j.molcel.2021.09.002; GPMDB: 30.
Gao Z, et al. (2021) "A Quantitative Proteomic Approach for the Identification of DNA Guanine Quadruplex-Binding Proteins." J Proteome Res 20(11):4919–4924; PMID: 34570971; doi: 10.1021/acs.jproteome.1c00603; GPMDB: 30.
Gomkale R, et al. (2021) "Mapping protein interactions in the active TOM-TIM23 supercomplex." Nat Commun 12(1):5715; PMID: 34588454; doi: 10.1038/s41467-021-26016-1; GPMDB: 87.
Kim M, et al. (2021) "A protein interaction landscape of breast cancer." Science 374(6563):eabf3066; PMID: 34591612; doi: 10.1126/science.abf3066; GPMDB: 702.
Swaney DL, et al. (2021) "A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity." Science 374(6563):eabf2911; PMID: 34591642; doi: 10.1126/science.abf2911; GPMDB: 551.
Stieglitz F, et al. (2021) "The Binary Toxin of Clostridioides difficile Alters the Proteome and Phosphoproteome of HEp-2 Cells." Front Microbiol 12:725612; PMID: 34594315; doi: 10.3389/fmicb.2021.725612; GPMDB: 57.
Ross SH, et al. (2021) "Quantitative Analyses Reveal How Hypoxia Reconfigures the Proteome of Primary Cytotoxic T Lymphocytes." Front Immunol 12:712402; PMID: 34603285; doi: 10.3389/fimmu.2021.712402; GPMDB: 6.
Yau B, et al. (2021) "Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet." iScience 24(10):103099; PMID: 34622154; doi: 10.1016/j.isci.2021.103099; GPMDB: 38.
Di Persio S, et al. (2021) "Single-cell RNA-seq unravels alterations of the human spermatogonial stem cell compartment in patients with impaired spermatogenesis." Cell Rep Med 2(9):100395; PMID: 34622232; doi: 10.1016/j.xcrm.2021.100395; GPMDB: 2.
Lorente E, et al. (2021) "Acid Stripping after Infection Improves the Detection of Viral HLA Class I Natural Ligands Identified by Mass Spectrometry." Int J Mol Sci 22(19):; PMID: 34638844; doi: 10.3390/ijms221910503; GPMDB: 12.
Zhang YH, et al. (2021) "Lung proteomic biomarkers associated with chronic obstructive pulmonary disease." Am J Physiol Lung Cell Mol Physiol 321(6):L1119–L1130; PMID: 34668408; doi: 10.1152/ajplung.00198.2021; GPMDB: 456.
Lu C, et al. (2021) "Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms." J Proteome Res 20(11):5203–5211; PMID: 34669412; doi: 10.1021/acs.jproteome.1c00624; GPMDB: 192.
Saburina IN, et al. (2021) "Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three-dimensional culture." Proteomics :e2000304; PMID: 34674377; doi: 10.1002/pmic.202000304; GPMDB: 20.
Wang Y, et al. (2021) "SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells." Nature 599(7883):136–140; PMID: 34707288; doi: 10.1038/s41586-021-04025-w; GPMDB: 2.
Biswas D, et al. (2021) "Deciphering the Interregional and Interhemisphere Proteome of the Human Brain in the Context of the Human Proteome Project." J Proteome Res 20(12):5280–5293; PMID: 34714085; doi: 10.1021/acs.jproteome.1c00511; GPMDB: 80.
Sirois I, et al. (2021) "Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis." J Vis Exp (176):; PMID: 34723952; doi: 10.3791/63052; GPMDB: 38.
Leung MR, et al. (2021) "In-cell structures of conserved supramolecular protein arrays at the mitochondria-cytoskeleton interface in mammalian sperm." Proc Natl Acad Sci U S A 118(45):; PMID: 34737233; doi: 10.1073/pnas.2110996118; GPMDB: 6.
Yap K, et al. (2021) "Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments." Mol Cell; PMID: 34741808; doi: 10.1016/j.molcel.2021.10.009; GPMDB: 18.
Shlomovitz I, et al. (2021) "Proteomic analysis of necroptotic extracellular vesicles." Cell Death Dis 12(11):1059; PMID: 34750357; doi: 10.1038/s41419-021-04317-z; GPMDB: 12.
Froehlich JW, et al. (2021) "The Urinary Proteomic Profile Implicates Key Regulators for Urologic Chronic Pelvic Pain Syndrome (UCPPS): A MAPP Research Network Study." Mol Cell Proteomics 21(1):100176; PMID: 34774759; doi: 10.1016/j.mcpro.2021.100176; GPMDB: 52.
Capizzi M, et al. (2021) "Developmental defects in Huntington's disease show that axonal growth and microtubule reorganization require NUMA1." Neuron; PMID: 34793694; doi: 10.1016/j.neuron.2021.10.033; GPMDB: 10.
Stirm M, et al. (2021) "A scalable, clinically severe pig model for Duchenne muscular dystrophy." Dis Model Mech 14(12):; PMID: 34796900; doi: 10.1242/dmm.049285; GPMDB: 42.
Morgenstern M, et al. (2021) "Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context." Cell Metab 33(12):2464–2483.e18; PMID: 34800366; doi: 10.1016/j.cmet.2021.11.001; GPMDB: 1024.
de Sousa BM, et al. (2021) "Capacitive interdigitated system of high osteoinductive/conductive performance for personalized acting-sensing implants." NPJ Regen Med 6(1):80; PMID: 34815414; doi: 10.1038/s41536-021-00184-6; GPMDB: 8.
Ding Y, et al. (2021) "MicroRNA-222 Transferred From Semen Extracellular Vesicles Inhibits Sperm Apoptosis by Targeting BCL2L11." Front Cell Dev Biol 9:736864; PMID: 34820370; doi: 10.3389/fcell.2021.736864; GPMDB: 8.
Rolfs Z, et al. (2021) "An atlas of protein turnover rates in mouse tissues." Nat Commun 12(1):6778; PMID: 34836951; doi: 10.1038/s41467-021-26842-3; GPMDB: 173.
Needham EJ, et al. (2021) "Personalized phosphoproteomics identifies functional signaling." Nat Biotechnol; PMID: 34857927; doi: 10.1038/s41587-021-01099-9; GPMDB: 26.
Ziemlińska E, et al. (2021) "Palm Oil-Rich Diet Affects Murine Liver Proteome and S-Palmitoylome." Int J Mol Sci 22(23):; PMID: 34884899; doi: 10.3390/ijms222313094; GPMDB: 24.
Taher L, et al. (2021) "The proteome, not the transcriptome, predicts that oocyte superovulation affects embryonic phenotypes in mice." Sci Rep 11(1):23731; PMID: 34887460; doi: 10.1038/s41598-021-03054-9; GPMDB: 28.
Almeida N, et al. (2021) "Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database." Cancers (Basel) 13(24):; PMID: 34944842; doi: 10.3390/cancers13246224; GPMDB: 24.
Halkoum R, et al. (2021) "Glyoxal induces senescence in human keratinocytes through oxidative stress and activation of the AKT/FOXO3a/p27^KIP1 pathway." J Invest Dermatol; PMID: 34971698; doi: 10.1016/j.jid.2021.12.022; GPMDB: 4.

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 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 Jan 2, 2022.
+#Lipton MS, <i>et al.</i> (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: [https://pubmed.ncbi.nlm.nih.gov/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498].
+#Liu T, <i>et al.</i> (2004) &quot;High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology.&quot; <i>Anal Chem</i> <b>76</b>(18):5345&ndash;53; PMID: [https://pubmed.ncbi.nlm.nih.gov/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/15362891 6].
+#Sauer G, <i>et al.</i> (2005) &quot;Proteome analysis of the human mitotic spindle.&quot; <i>Mol Cell Proteomics</i> <b>4</b>(1):35&ndash;43; PMID: [https://pubmed.ncbi.nlm.nih.gov/15561729 15561729]; doi: [https://dx.doi.org/10.1074/mcp.M400158-MCP200 10.1074/mcp.M400158-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/15561729 1].
+#Klein C, <i>et al.</i> (2005) &quot;The membrane proteome of Halobacterium salinarum.&quot; <i>Proteomics</i> <b>5</b>(1):180&ndash;97; PMID: [https://pubmed.ncbi.nlm.nih.gov/15619294 15619294]; doi: [https://dx.doi.org/10.1002/pmic.200400943 10.1002/pmic.200400943]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/15619294 37].
+#Searle BC, <i>et al.</i> (2005) &quot;Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm.&quot; <i>J Proteome Res</i> <b>4</b>(2):546&ndash;54; PMID: [https://pubmed.ncbi.nlm.nih.gov/15822933 15822933]; doi: [https://dx.doi.org/10.1021/pr049781j 10.1021/pr049781j]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/15822933 4].
+#Elias JE, <i>et al.</i> (2005) &quot;Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations.&quot; <i>Nat Methods</i> <b>2</b>(9):667&ndash;75; PMID: [https://pubmed.ncbi.nlm.nih.gov/16118637 16118637]; doi: [https://dx.doi.org/10.1038/nmeth785 10.1038/nmeth785]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16118637 30].
+#Lee YJ, <i>et al.</i> (2006) &quot;Proteome analysis of human hair shaft: from protein identification to posttranslational modification.&quot; <i>Mol Cell Proteomics</i> <b>5</b>(5):789&ndash;800; PMID: [https://pubmed.ncbi.nlm.nih.gov/16446289 16446289]; doi: [https://dx.doi.org/10.1074/mcp.M500278-MCP200 10.1074/mcp.M500278-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16446289 75].
+#Gatlin CL, <i>et al.</i> (2006) &quot;Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus.&quot; <i>Proteomics</i> <b>6</b>(5):1530&ndash;49; PMID: [https://pubmed.ncbi.nlm.nih.gov/16470658 16470658]; doi: [https://dx.doi.org/10.1002/pmic.200500253 10.1002/pmic.200500253]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16470658 1603].
+#Keshamouni VG, <i>et al.</i> (2006) &quot;Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype.&quot; <i>J Proteome Res</i> <b>5</b>(5):1143&ndash;54; PMID: [https://pubmed.ncbi.nlm.nih.gov/16674103 16674103]; doi: [https://dx.doi.org/10.1021/pr050455t 10.1021/pr050455t]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16674103 3].
+#Bisle B, <i>et al.</i> (2006) &quot;Quantitative profiling of the membrane proteome in a halophilic archaeon.&quot; <i>Mol Cell Proteomics</i> <b>5</b>(9):1543&ndash;58; PMID: [https://pubmed.ncbi.nlm.nih.gov/16804162 16804162]; doi: [https://dx.doi.org/10.1074/mcp.M600106-MCP200 10.1074/mcp.M600106-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16804162 32].
+#Hamacher M, <i>et al.</i> (2006) &quot;HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.&quot; <i>Proteomics</i> <b>6</b>(18):4890&ndash;8; PMID: [https://pubmed.ncbi.nlm.nih.gov/16927433 16927433]; doi: [https://dx.doi.org/10.1002/pmic.200600295 10.1002/pmic.200600295]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16927433 296].
+#Beausoleil SA, <i>et al.</i> (2006) &quot;A probability-based approach for high-throughput protein phosphorylation analysis and site localization.&quot; <i>Nat Biotechnol</i> <b>24</b>(10):1285&ndash;92; PMID: [https://pubmed.ncbi.nlm.nih.gov/16964243 16964243]; doi: [https://dx.doi.org/10.1038/nbt1240 10.1038/nbt1240]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16964243 31].
+#Whitehead K, <i>et al.</i> (2006) &quot;An integrated systems approach for understanding cellular responses to gamma radiation.&quot; <i>Mol Syst Biol</i> <b>2</b>:47; PMID: [https://pubmed.ncbi.nlm.nih.gov/16969339 16969339]; doi: [https://dx.doi.org/10.1038/msb4100091 10.1038/msb4100091]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/16969339 27].
+#Price TS, <i>et al.</i> (2007) &quot;EBP, a program for protein identification using multiple tandem mass spectrometry datasets.&quot; <i>Mol Cell Proteomics</i> <b>6</b>(3):527&ndash;36; PMID: [https://pubmed.ncbi.nlm.nih.gov/17164401 17164401]; doi: [https://dx.doi.org/10.1074/mcp.T600049-MCP200 10.1074/mcp.T600049-MCP200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17164401 314].
+#Tanner S, <i>et al.</i> (2007) &quot;Improving gene annotation using peptide mass spectrometry.&quot; <i>Genome Res</i> <b>17</b>(2):231&ndash;9; PMID: [https://pubmed.ncbi.nlm.nih.gov/17189379 17189379]; doi: [https://dx.doi.org/10.1101/gr.5646507 10.1101/gr.5646507]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/17189379 1].
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