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==Data from publications== | ==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 Dec. | + | 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 Dec. 24, 2017. |
#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." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #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." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#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." <i>Mol Cell</i> <b>67</b>(2):294–307.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648780 28648780]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.026 10.1016/j.molcel.2017.05.026]; GPMDB: [http://gpmdb.org/data/keyword/28648780 50]. | #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." <i>Mol Cell</i> <b>67</b>(2):294–307.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648780 28648780]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.026 10.1016/j.molcel.2017.05.026]; GPMDB: [http://gpmdb.org/data/keyword/28648780 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." <i>Cell Rep</i> <b>19</b>(13):2836–2852; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28658629 28658629]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.06.014 10.1016/j.celrep.2017.06.014]; GPMDB: [http://gpmdb.org/data/keyword/28658629 697]. | #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." <i>Cell Rep</i> <b>19</b>(13):2836–2852; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28658629 28658629]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.06.014 10.1016/j.celrep.2017.06.014]; GPMDB: [http://gpmdb.org/data/keyword/28658629 697]. | ||
+ | #Offenburger SL, Bensaddek D, Murillo AB, Lamond AI, Gartner A, (2017) "Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development." <i>Sci Rep</i> <b>7</b>(1):4314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28659600 28659600]; doi: [https://dx.doi.org/10.1038/s41598-017-04375-4 10.1038/s41598-017-04375-4]; GPMDB: [http://gpmdb.org/data/keyword/28659600 289]. | ||
#Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D, (2017) "Comparison of fractionation proteomics for local SWATH library building." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28664598 28664598]; doi: [https://dx.doi.org/10.1002/pmic.201700052 10.1002/pmic.201700052]; GPMDB: [http://gpmdb.org/data/keyword/28664598 4]. | #Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D, (2017) "Comparison of fractionation proteomics for local SWATH library building." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28664598 28664598]; doi: [https://dx.doi.org/10.1002/pmic.201700052 10.1002/pmic.201700052]; GPMDB: [http://gpmdb.org/data/keyword/28664598 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." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28665616 28665616]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00156 10.1021/acs.jproteome.7b00156]; GPMDB: [http://gpmdb.org/data/keyword/28665616 290]. | #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." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28665616 28665616]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00156 10.1021/acs.jproteome.7b00156]; GPMDB: [http://gpmdb.org/data/keyword/28665616 290]. | ||
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#Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T, (2017) "Detergent-insoluble proteome analysis revealed aberrantly aggregated proteins in human preeclampsia placentas." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28965414 28965414]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00352 10.1021/acs.jproteome.7b00352]; GPMDB: [http://gpmdb.org/data/keyword/28965414 4]. | #Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T, (2017) "Detergent-insoluble proteome analysis revealed aberrantly aggregated proteins in human preeclampsia placentas." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28965414 28965414]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00352 10.1021/acs.jproteome.7b00352]; GPMDB: [http://gpmdb.org/data/keyword/28965414 4]. | ||
#Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD, (2017) "Identifying host factors associated with DNA replicated during virus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28972080 28972080]; doi: [https://dx.doi.org/10.1074/mcp.M117.067116 10.1074/mcp.M117.067116]; GPMDB: [http://gpmdb.org/data/keyword/28972080 164]. | #Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD, (2017) "Identifying host factors associated with DNA replicated during virus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28972080 28972080]; doi: [https://dx.doi.org/10.1074/mcp.M117.067116 10.1074/mcp.M117.067116]; GPMDB: [http://gpmdb.org/data/keyword/28972080 164]. | ||
- | #Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA, (2017) "Systems-level identification of PKA-dependent signaling in epithelial cells." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(42):E8875–E8884; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28973931 28973931]; doi: [https://dx.doi.org/10.1073/pnas.1709123114 10.1073/pnas.1709123114]; GPMDB: [http://gpmdb.org/data/keyword/28973931 | + | #Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA, (2017) "Systems-level identification of PKA-dependent signaling in epithelial cells." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(42):E8875–E8884; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28973931 28973931]; doi: [https://dx.doi.org/10.1073/pnas.1709123114 10.1073/pnas.1709123114]; GPMDB: [http://gpmdb.org/data/keyword/28973931 73]. |
#Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | #Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | ||
#Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | #Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | ||
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#van der Wal L, Bezstarosti K, Sap KA, Dekkers DHW, Rijkers E, Mientjes E, Elgersma Y, Demmers JAA, (2017) "Improvement of ubiquitylation site detection by Orbitrap mass spectrometry." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29122726 29122726]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.014 10.1016/j.jprot.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29122726 86]. | #van der Wal L, Bezstarosti K, Sap KA, Dekkers DHW, Rijkers E, Mientjes E, Elgersma Y, Demmers JAA, (2017) "Improvement of ubiquitylation site detection by Orbitrap mass spectrometry." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29122726 29122726]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.014 10.1016/j.jprot.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29122726 86]. | ||
#Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M, (2017) "Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29125462 29125462]; doi: [https://dx.doi.org/10.7554/eLife.31012 10.7554/eLife.31012]; GPMDB: [http://gpmdb.org/data/keyword/29125462 667]. | #Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M, (2017) "Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29125462 29125462]; doi: [https://dx.doi.org/10.7554/eLife.31012 10.7554/eLife.31012]; GPMDB: [http://gpmdb.org/data/keyword/29125462 667]. | ||
+ | #Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M, (2017) "A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29128334 29128334]; doi: [https://dx.doi.org/10.1016/j.cels.2017.10.010 10.1016/j.cels.2017.10.010]; GPMDB: [http://gpmdb.org/data/keyword/29128334 109]. | ||
#García-Berrocoso T, Llombart V, Colàs-Campàs L, Hainard A, Licker V, Penalba A, Ramiro L, Simats A, Bustamante A, Martínez-Saez E, Canals F, Sanchez JC, Montaner J, (2017) "Single Cell Immuno-laser Microdissection Coupled to Label-free Proteomics to Reveal the Proteotypes of Human Brain Cells After Ischemia." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133510 29133510]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000419 10.1074/mcp.RA117.000419]; GPMDB: [http://gpmdb.org/data/keyword/29133510 102]. | #García-Berrocoso T, Llombart V, Colàs-Campàs L, Hainard A, Licker V, Penalba A, Ramiro L, Simats A, Bustamante A, Martínez-Saez E, Canals F, Sanchez JC, Montaner J, (2017) "Single Cell Immuno-laser Microdissection Coupled to Label-free Proteomics to Reveal the Proteotypes of Human Brain Cells After Ischemia." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133510 29133510]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000419 10.1074/mcp.RA117.000419]; GPMDB: [http://gpmdb.org/data/keyword/29133510 102]. | ||
#Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [http://gpmdb.org/data/keyword/29133896 8]. | #Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [http://gpmdb.org/data/keyword/29133896 8]. | ||
Line 1,726: | Line 1,728: | ||
#Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [http://gpmdb.org/data/keyword/29189203 4]. | #Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [http://gpmdb.org/data/keyword/29189203 4]. | ||
#Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [http://gpmdb.org/data/keyword/29191878 3032]. | #Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [http://gpmdb.org/data/keyword/29191878 3032]. | ||
+ | #Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S, (2017) "Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome." <i>J Proteomics</i> <b>173</b>:89–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208510 29208510]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.025 10.1016/j.jprot.2017.11.025]; GPMDB: [http://gpmdb.org/data/keyword/29208510 72]. | ||
+ | #Wierer M, Prestel M, Schiller H, Yan G, Schaab C, Azghandi S, Werner J, Kessler T, Malik R, Murgia M, Aherrahrou Z, Schunkert H, Dichgans M, Mann M, (2017) "Compartment-resolved Proteomic Analysis of Mouse Aorta during Atherosclerotic Plaque Formation Reveals Osteoclast-specific Protein Expression." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208753 29208753]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000315 10.1074/mcp.RA117.000315]; GPMDB: [http://gpmdb.org/data/keyword/29208753 156]. | ||
+ | #Krogager TP, Ernst RJ, Elliott TS, Calo L, Beránek V, Ciabatti E, Spillantini MG, Tripodi M, Hastings MH, Chin JW, (2017) "Labeling and identifying cell-specific proteomes in the mouse brain." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29251727 29251727]; doi: [https://dx.doi.org/10.1038/nbt.4056 10.1038/nbt.4056]; GPMDB: [http://gpmdb.org/data/keyword/29251727 33]. |
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 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.
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 Dec. 24, 2017.