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==Data from publications== | ==Data from publications== | ||
- | The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of January | + | The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of January 14, 2016. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, <i>Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.</i> Proc Natl Acad Sci U S A (2002) <b>99</b>(17): 11049-54; <i>PMID:12177431; doi: 10.1073/pnas.172170199. GPMDB files: [http://gpmdb.org/data/keyword/12177431 498]</i>. | #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, <i>Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.</i> Proc Natl Acad Sci U S A (2002) <b>99</b>(17): 11049-54; <i>PMID:12177431; doi: 10.1073/pnas.172170199. GPMDB files: [http://gpmdb.org/data/keyword/12177431 498]</i>. | ||
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#Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R, <i>Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.</i> Mol Cell Proteomics (2013) <b>12</b>(6): 1741-51; <i>PMID:23462206; doi: 10.1074/mcp.M112.023754. GPMDB files: [http://gpmdb.org/data/keyword/23462206 384]</i>. | #Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R, <i>Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas.</i> Mol Cell Proteomics (2013) <b>12</b>(6): 1741-51; <i>PMID:23462206; doi: 10.1074/mcp.M112.023754. GPMDB files: [http://gpmdb.org/data/keyword/23462206 384]</i>. | ||
#Hassan C, Kester MG, de Ru AH, Hombrink P, Drijfhout JW, Nijveen H, Leunissen JA, Heemskerk MH, Falkenburg JH, van Veelen PA, <i>The human leukocyte antigen-presented ligandome of B lymphocytes.</i> Mol Cell Proteomics (2013) <b>12</b>(7): 1829-43; <i>PMID:23481700; doi: 10.1074/mcp.M112.024810. GPMDB files: [http://gpmdb.org/data/keyword/23481700 191]</i>. | #Hassan C, Kester MG, de Ru AH, Hombrink P, Drijfhout JW, Nijveen H, Leunissen JA, Heemskerk MH, Falkenburg JH, van Veelen PA, <i>The human leukocyte antigen-presented ligandome of B lymphocytes.</i> Mol Cell Proteomics (2013) <b>12</b>(7): 1829-43; <i>PMID:23481700; doi: 10.1074/mcp.M112.024810. GPMDB files: [http://gpmdb.org/data/keyword/23481700 191]</i>. | ||
- | #Urbaniak MD, Martin DM, Ferguson MA, <i>Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei.</i> J Proteome Res (2013) <b>12</b>(5): 2233-44; <i>PMID:23485197; doi: 10.1021/pr400086y. GPMDB files: [http://gpmdb.org/data/keyword/23485197 | + | #Urbaniak MD, Martin DM, Ferguson MA, <i>Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei.</i> J Proteome Res (2013) <b>12</b>(5): 2233-44; <i>PMID:23485197; doi: 10.1021/pr400086y. GPMDB files: [http://gpmdb.org/data/keyword/23485197 148]</i>. |
#van Nuland R, Smits AH, Pallaki P, Jansen PW, Vermeulen M, Timmers HT, <i>Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes.</i> Mol Cell Biol (2013) <b>33</b>(10): 2067-77; <i>PMID:23508102; doi: 10.1128/MCB.01742-12. GPMDB files: [http://gpmdb.org/data/keyword/23508102 52]</i>. | #van Nuland R, Smits AH, Pallaki P, Jansen PW, Vermeulen M, Timmers HT, <i>Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes.</i> Mol Cell Biol (2013) <b>33</b>(10): 2067-77; <i>PMID:23508102; doi: 10.1128/MCB.01742-12. GPMDB files: [http://gpmdb.org/data/keyword/23508102 52]</i>. | ||
#Papachristou EK, Roumeliotis TI, Chrysagi A, Trigoni C, Charvalos E, Townsend PA, Pavlakis K, Garbis SD, <i>The shotgun proteomic study of the human ThinPrep cervical smear using iTRAQ mass-tagging and 2D LC-FT-Orbitrap-MS: the detection of the human papillomavirus at the protein level.</i> J Proteome Res (2013) <b>12</b>(5): 2078-89; <i>PMID:23510160; doi: 10.1021/pr301067r. GPMDB files: [http://gpmdb.org/data/keyword/23510160 3]</i>. | #Papachristou EK, Roumeliotis TI, Chrysagi A, Trigoni C, Charvalos E, Townsend PA, Pavlakis K, Garbis SD, <i>The shotgun proteomic study of the human ThinPrep cervical smear using iTRAQ mass-tagging and 2D LC-FT-Orbitrap-MS: the detection of the human papillomavirus at the protein level.</i> J Proteome Res (2013) <b>12</b>(5): 2078-89; <i>PMID:23510160; doi: 10.1021/pr301067r. GPMDB files: [http://gpmdb.org/data/keyword/23510160 3]</i>. | ||
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#Oberbach A, Adams V, Schlichting N, Heinrich M, Kullnick Y, Lehmann S, Lehmann S, Feder S, Correia JC, Mohr FW, Völker U, Jehmlich N, <i>Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins.</i> Clin Chim Acta (2015) <b>453</b>: 114-122; <i>PMID:26688386; doi: 10.1016/j.cca.2015.12.005. GPMDB files: [http://gpmdb.org/data/keyword/26688386 10]</i>. | #Oberbach A, Adams V, Schlichting N, Heinrich M, Kullnick Y, Lehmann S, Lehmann S, Feder S, Correia JC, Mohr FW, Völker U, Jehmlich N, <i>Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins.</i> Clin Chim Acta (2015) <b>453</b>: 114-122; <i>PMID:26688386; doi: 10.1016/j.cca.2015.12.005. GPMDB files: [http://gpmdb.org/data/keyword/26688386 10]</i>. | ||
#Eitzinger N, Wagner V, Weisheit W, Geimer S, Boness D, Kreimer G, Mittag M, <i>Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation.</i> Front Plant Sci (2015) <b>6</b>: 1085; <i>PMID:26697039; doi: 10.3389/fpls.2015.01085. GPMDB files: [http://gpmdb.org/data/keyword/26697039 128]</i>. | #Eitzinger N, Wagner V, Weisheit W, Geimer S, Boness D, Kreimer G, Mittag M, <i>Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation.</i> Front Plant Sci (2015) <b>6</b>: 1085; <i>PMID:26697039; doi: 10.3389/fpls.2015.01085. GPMDB files: [http://gpmdb.org/data/keyword/26697039 128]</i>. | ||
- | #Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin MF, <i>ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen.</i> Mol Cell Proteomics (2015) ; <i>PMID:26699800; doi: 10.1074/mcp.M115.055723. GPMDB files: [http://gpmdb.org/data/keyword/26699800 | + | #Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin MF, <i>ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen.</i> Mol Cell Proteomics (2015) ; <i>PMID:26699800; doi: 10.1074/mcp.M115.055723. GPMDB files: [http://gpmdb.org/data/keyword/26699800 141]</i>. |
#Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, <i>Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome.</i> Proteomics (2015) ; <i>PMID:26702875; doi: 10.1002/pmic.201500187. GPMDB files: [http://gpmdb.org/data/keyword/26702875 2]</i>. | #Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, <i>Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome.</i> Proteomics (2015) ; <i>PMID:26702875; doi: 10.1002/pmic.201500187. GPMDB files: [http://gpmdb.org/data/keyword/26702875 2]</i>. | ||
#Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, <i>Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains.</i> Mol Cell (2016) <b>61</b>(1): 125-37; <i>PMID:26711008; doi: 10.1016/j.molcel.2015.11.016. GPMDB files: [http://gpmdb.org/data/keyword/26711008 44]</i>. | #Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, <i>Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains.</i> Mol Cell (2016) <b>61</b>(1): 125-37; <i>PMID:26711008; doi: 10.1016/j.molcel.2015.11.016. GPMDB files: [http://gpmdb.org/data/keyword/26711008 44]</i>. | ||
+ | #Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Mueller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G, <i>An inducible retroviral expression system for tandem affinity purification mass-spectrometry-based proteomics identifies MLKL as an HSP90 client.</i> Mol Cell Proteomics (2015) ; <i>PMID:26714523; doi: 10.1074/mcp.O115.055350. GPMDB files: [http://gpmdb.org/data/keyword/26714523 16]</i>. | ||
+ | #Bode D, Yu L, Tate P, Pardo M, Choudhary JS, <i>Characterisation of two distinct Nucleosome Remodelling and Deacetylase Complex (NuRD) assemblies in embryonic stem cells.</i> Mol Cell Proteomics (2015) ; <i>PMID:26714524; doi: 10.1074/mcp.M115.053207. GPMDB files: [http://gpmdb.org/data/keyword/26714524 179]</i>. | ||
#Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV, <i>Protein turnover during in vitro tissue engineering.</i> Biomaterials (2015) <b>81</b>: 104-113; <i>PMID:26724458; doi: 10.1016/j.biomaterials.2015.12.004. GPMDB files: [http://gpmdb.org/data/keyword/26724458 66]</i>. | #Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV, <i>Protein turnover during in vitro tissue engineering.</i> Biomaterials (2015) <b>81</b>: 104-113; <i>PMID:26724458; doi: 10.1016/j.biomaterials.2015.12.004. GPMDB files: [http://gpmdb.org/data/keyword/26724458 66]</i>. | ||
- | #Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, <i>Proteomic maps of breast cancer subtypes.</i> Nat Commun (2016) <b>7</b>: 10259; <i>PMID:26725330; doi: 10.1038/ncomms10259. GPMDB files: [http://gpmdb.org/data/keyword/26725330 | + | #Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, <i>Proteomic maps of breast cancer subtypes.</i> Nat Commun (2016) <b>7</b>: 10259; <i>PMID:26725330; doi: 10.1038/ncomms10259. GPMDB files: [http://gpmdb.org/data/keyword/26725330 207]</i>. |
+ | #Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, <i>DCAF1 controls T-cell function via p53-dependent and -independent mechanisms.</i> Nat Commun (2016) <b>7</b>: 10307; <i>PMID:26728942; doi: 10.1038/ncomms10307. GPMDB files: [http://gpmdb.org/data/keyword/26728942 118]</i>. | ||
+ | #Clark DJ, Fondrie WE, Yang A, Mao L, <i>Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes.</i> J Proteomics (2015) ; <i>PMID:26739763; doi: 10.1016/j.jprot.2015.12.023. GPMDB files: [http://gpmdb.org/data/keyword/26739763 3]</i>. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a 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 January 14, 2016.