Line 25: | Line 25: | ||
==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 April | + | 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 April 16, 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]. | ||
Line 1,137: | Line 1,137: | ||
#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." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(8):E968–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26858453 26858453]; doi: [https://dx.doi.org/10.1073/pnas.1521230113 10.1073/pnas.1521230113]; GPMDB: [http://gpmdb.org/data/keyword/26858453 56]. | #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." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(8):E968–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26858453 26858453]; doi: [https://dx.doi.org/10.1073/pnas.1521230113 10.1073/pnas.1521230113]; GPMDB: [http://gpmdb.org/data/keyword/26858453 56]. | ||
#Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | #Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | ||
- | #Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein." <i>J Biol Chem</i> <b>291</b>(13):7045–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 | + | #Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein." <i>J Biol Chem</i> <b>291</b>(13):7045–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 120]. |
#Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A, (2015) "Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods." <i>Data Brief</i> <b>6</b>:286–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26862574 26862574]; doi: [https://dx.doi.org/10.1016/j.dib.2015.11.063 10.1016/j.dib.2015.11.063]; GPMDB: [http://gpmdb.org/data/keyword/26862574 27]. | #Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A, (2015) "Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods." <i>Data Brief</i> <b>6</b>:286–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26862574 26862574]; doi: [https://dx.doi.org/10.1016/j.dib.2015.11.063 10.1016/j.dib.2015.11.063]; GPMDB: [http://gpmdb.org/data/keyword/26862574 27]. | ||
#Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | #Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | ||
Line 1,502: | Line 1,502: | ||
#Winter M, Dokic I, Schlegel J, Warnken U, Debus J, Abdollahi A, Schnölzer M, (2017) "Deciphering the acute cellular phosphoproteome response to irradiation with X-rays, protons and carbon ions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28302921 28302921]; doi: [https://dx.doi.org/10.1074/mcp.M116.066597 10.1074/mcp.M116.066597]; GPMDB: [http://gpmdb.org/data/keyword/28302921 269]. | #Winter M, Dokic I, Schlegel J, Warnken U, Debus J, Abdollahi A, Schnölzer M, (2017) "Deciphering the acute cellular phosphoproteome response to irradiation with X-rays, protons and carbon ions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28302921 28302921]; doi: [https://dx.doi.org/10.1074/mcp.M116.066597 10.1074/mcp.M116.066597]; GPMDB: [http://gpmdb.org/data/keyword/28302921 269]. | ||
#Kliza K, Taumer C, Pinzuti I, Franz-Wachtel M, Kunzelmann S, Stieglitz B, Macek B, Husnjak K, (2017) "Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28319114 28319114]; doi: [https://dx.doi.org/10.1038/nmeth.4228 10.1038/nmeth.4228]; GPMDB: [http://gpmdb.org/data/keyword/28319114 32]. | #Kliza K, Taumer C, Pinzuti I, Franz-Wachtel M, Kunzelmann S, Stieglitz B, Macek B, Husnjak K, (2017) "Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28319114 28319114]; doi: [https://dx.doi.org/10.1038/nmeth.4228 10.1038/nmeth.4228]; GPMDB: [http://gpmdb.org/data/keyword/28319114 32]. | ||
+ | #Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali F, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U, (2017) "Quantitative tyrosine phosphoproteomics of EGFR tyrosine kinase inhibitor-treated lung adenocarcinoma cells reveals potential novel biomarkers of therapeutic response." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28331001 28331001]; doi: [https://dx.doi.org/10.1074/mcp.M117.067439 10.1074/mcp.M117.067439]; GPMDB: [http://gpmdb.org/data/keyword/28331001 41]. | ||
+ | #Nathan A, Reinhardt P, Kruspe D, Jörß T, Groth M, Nolte H, Habenicht A, Herrmann J, Holschbach V, Toth B, Krüger M, Wang ZQ, Platzer M, Englert C, (2017) "The Wilms tumor protein Wt1 contributes to female fertility by regulating oviductal proteostasis." <i>Hum Mol Genet</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28334862 28334862]; doi: [https://dx.doi.org/10.1093/hmg/ddx075 10.1093/hmg/ddx075]; GPMDB: [http://gpmdb.org/data/keyword/28334862 48]. | ||
#Tien JF, Mazloomian A, Cheng SG, Hughes CS, Chow CC, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VC, Shah SP, Aparicio S, Morin GB, (2017) "CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28334900 28334900]; doi: [https://dx.doi.org/10.1093/nar/gkx187 10.1093/nar/gkx187]; GPMDB: [http://gpmdb.org/data/keyword/28334900 11]. | #Tien JF, Mazloomian A, Cheng SG, Hughes CS, Chow CC, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VC, Shah SP, Aparicio S, Morin GB, (2017) "CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28334900 28334900]; doi: [https://dx.doi.org/10.1093/nar/gkx187 10.1093/nar/gkx187]; GPMDB: [http://gpmdb.org/data/keyword/28334900 11]. | ||
#O'Neill JR, Pak HS, Pairo-Castineira E, Save V, Paterson-Brown S, Nenutil R, Vojtěšek B, Overton I, Scherl A, Hupp TR, (2017) "Quantitative shotgun proteomics unveils candidate novel oesophageal adenocarcinoma-specific proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28336725 28336725]; doi: [https://dx.doi.org/10.1074/mcp.M116.065078 10.1074/mcp.M116.065078]; GPMDB: [http://gpmdb.org/data/keyword/28336725 7]. | #O'Neill JR, Pak HS, Pairo-Castineira E, Save V, Paterson-Brown S, Nenutil R, Vojtěšek B, Overton I, Scherl A, Hupp TR, (2017) "Quantitative shotgun proteomics unveils candidate novel oesophageal adenocarcinoma-specific proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28336725 28336725]; doi: [https://dx.doi.org/10.1074/mcp.M116.065078 10.1074/mcp.M116.065078]; GPMDB: [http://gpmdb.org/data/keyword/28336725 7]. | ||
- | #Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV, (2017) "Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer." <i>Cell Rep</i> <b>18</b>(13):3242–3256; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28355574 28355574]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.015 10.1016/j.celrep.2017.03.015]; GPMDB: [http://gpmdb.org/data/keyword/28355574 | + | #Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV, (2017) "Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer." <i>Cell Rep</i> <b>18</b>(13):3242–3256; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28355574 28355574]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.015 10.1016/j.celrep.2017.03.015]; GPMDB: [http://gpmdb.org/data/keyword/28355574 59]. |
+ | #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 <i>Drosophila melanogaster</i>." <i>Genome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28381612 28381612]; doi: [https://dx.doi.org/10.1101/gr.213694.116 10.1101/gr.213694.116]; GPMDB: [http://gpmdb.org/data/keyword/28381612 124]. | ||
+ | #Chiang CK, Xu B, Mehta N, Mayne J, Sun WY, Cheng K, Ning Z, Dong J, Zou H, Cheng HM, Figeys D, (2017) "Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus." <i>Front Neurol</i> <b>8</b>:110; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28382018 28382018]; doi: [https://dx.doi.org/10.3389/fneur.2017.00110 10.3389/fneur.2017.00110]; GPMDB: [http://gpmdb.org/data/keyword/28382018 149]. |
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.
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 April 16, 2017.