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 | + | 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 June 4, 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 1,259: | Line 1,259: | ||
#Chaubey PM, Hofstetter L, Roschitzki B, Stieger B, (2016) "Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver." <i>PLoS One</i> <b>11</b>(6):e0158033; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27347675 27347675]; doi: [https://dx.doi.org/10.1371/journal.pone.0158033 10.1371/journal.pone.0158033]; GPMDB: [http://gpmdb.org/data/keyword/27347675 60]. | #Chaubey PM, Hofstetter L, Roschitzki B, Stieger B, (2016) "Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver." <i>PLoS One</i> <b>11</b>(6):e0158033; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27347675 27347675]; doi: [https://dx.doi.org/10.1371/journal.pone.0158033 10.1371/journal.pone.0158033]; GPMDB: [http://gpmdb.org/data/keyword/27347675 60]. | ||
#Bespyatykh J, Shitikov E, Butenko I, Altukhov I, Alexeev D, Mokrousov I, Dogonadze M, Zhuravlev V, Yablonsky P, Ilina E, Govorun V, (2016) "Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster." <i>Sci Rep</i> <b>6</b>:28985; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27356881 27356881]; doi: [https://dx.doi.org/10.1038/srep28985 10.1038/srep28985]; GPMDB: [http://gpmdb.org/data/keyword/27356881 23]. | #Bespyatykh J, Shitikov E, Butenko I, Altukhov I, Alexeev D, Mokrousov I, Dogonadze M, Zhuravlev V, Yablonsky P, Ilina E, Govorun V, (2016) "Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster." <i>Sci Rep</i> <b>6</b>:28985; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27356881 27356881]; doi: [https://dx.doi.org/10.1038/srep28985 10.1038/srep28985]; GPMDB: [http://gpmdb.org/data/keyword/27356881 23]. | ||
+ | #Monks J, Dzieciatkowska M, Bales ES, Orlicky DJ, Wright RM, McManaman JL, (2016) "Xanthine oxidoreductase mediates membrane docking of milk-fat droplets but is not essential for apocrine lipid secretion." <i>J Physiol</i> <b>594</b>(20):5899–5921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27357166 27357166]; doi: [https://dx.doi.org/10.1113/JP272390 10.1113/JP272390]; GPMDB: [http://gpmdb.org/data/keyword/27357166 16]. | ||
#Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT, (2016) "Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation." <i>Am J Physiol Cell Physiol</i> <b>311</b>(3):C404–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27357545 27357545]; doi: [https://dx.doi.org/10.1152/ajpcell.00121.2016 10.1152/ajpcell.00121.2016]; GPMDB: [http://gpmdb.org/data/keyword/27357545 3]. | #Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT, (2016) "Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation." <i>Am J Physiol Cell Physiol</i> <b>311</b>(3):C404–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27357545 27357545]; doi: [https://dx.doi.org/10.1152/ajpcell.00121.2016 10.1152/ajpcell.00121.2016]; GPMDB: [http://gpmdb.org/data/keyword/27357545 3]. | ||
#Dudekula K, Le Bihan T, (2016) "Data from quantitative label free proteomics analysis of rat spleen." <i>Data Brief</i> <b>8</b>:494–500; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27358910 27358910]; doi: [https://dx.doi.org/10.1016/j.dib.2016.05.058 10.1016/j.dib.2016.05.058]; GPMDB: [http://gpmdb.org/data/keyword/27358910 17]. | #Dudekula K, Le Bihan T, (2016) "Data from quantitative label free proteomics analysis of rat spleen." <i>Data Brief</i> <b>8</b>:494–500; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27358910 27358910]; doi: [https://dx.doi.org/10.1016/j.dib.2016.05.058 10.1016/j.dib.2016.05.058]; GPMDB: [http://gpmdb.org/data/keyword/27358910 17]. | ||
Line 1,510: | Line 1,511: | ||
#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 59]. | #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]. | ||
+ | #Casanova R, Xia D, Rulle U, Nanni P, Grossmann J, Vrugt B, Wettstein R, Ballester R, Astolfo A, Weder W, Moch H, Stampanoni M, Beck AH, Soltermann A, (2017) "Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness." <i>Cancer Res</i> <b>77</b>(10):2585–2593; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28364001 28364001]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2363 10.1158/0008-5472.CAN-16-2363]; GPMDB: [http://gpmdb.org/data/keyword/28364001 49]. | ||
#Chatzinikolaou G, Apostolou Z, Aid-Pavlidis T, Ioannidou A, Karakasilioti I, Papadopoulos GL, Aivaliotis M, Tsekrekou M, Strouboulis J, Kosteas T, Garinis GA, (2017) "ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes." <i>Nat Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28368372 28368372]; doi: [https://dx.doi.org/10.1038/ncb3499 10.1038/ncb3499]; GPMDB: [http://gpmdb.org/data/keyword/28368372 146]. | #Chatzinikolaou G, Apostolou Z, Aid-Pavlidis T, Ioannidou A, Karakasilioti I, Papadopoulos GL, Aivaliotis M, Tsekrekou M, Strouboulis J, Kosteas T, Garinis GA, (2017) "ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes." <i>Nat Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28368372 28368372]; doi: [https://dx.doi.org/10.1038/ncb3499 10.1038/ncb3499]; GPMDB: [http://gpmdb.org/data/keyword/28368372 146]. | ||
#Duguet F, Locard-Paulet M, Marcellin M, Chaoui K, Bernard I, Andreoletti O, Lesourne R, Burlet-Schiltz O, Gonzalez de Peredo A, Saoudi A, (2017) "Proteomic analysis of regulatory T cells reveals the importance of Themis1 in the control of their suppressive function." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373295 28373295]; doi: [https://dx.doi.org/10.1074/mcp.M116.062745 10.1074/mcp.M116.062745]; GPMDB: [http://gpmdb.org/data/keyword/28373295 26]. | #Duguet F, Locard-Paulet M, Marcellin M, Chaoui K, Bernard I, Andreoletti O, Lesourne R, Burlet-Schiltz O, Gonzalez de Peredo A, Saoudi A, (2017) "Proteomic analysis of regulatory T cells reveals the importance of Themis1 in the control of their suppressive function." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373295 28373295]; doi: [https://dx.doi.org/10.1074/mcp.M116.062745 10.1074/mcp.M116.062745]; GPMDB: [http://gpmdb.org/data/keyword/28373295 26]. | ||
Line 1,529: | Line 1,531: | ||
#Beyene GT, Kalayou S, Riaz T, Tonjum T, (2017) "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis." <i>BMC Microbiol</i> <b>17</b>(1):96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431522 28431522]; doi: [https://dx.doi.org/10.1186/s12866-017-1004-8 10.1186/s12866-017-1004-8]; GPMDB: [http://gpmdb.org/data/keyword/28431522 108]. | #Beyene GT, Kalayou S, Riaz T, Tonjum T, (2017) "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis." <i>BMC Microbiol</i> <b>17</b>(1):96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431522 28431522]; doi: [https://dx.doi.org/10.1186/s12866-017-1004-8 10.1186/s12866-017-1004-8]; GPMDB: [http://gpmdb.org/data/keyword/28431522 108]. | ||
#Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [http://gpmdb.org/data/keyword/28455291 60]. | #Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [http://gpmdb.org/data/keyword/28455291 60]. | ||
+ | #Tran TT, Strozynski M, Thiede B, (2017) "Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28464451 28464451]; doi: [https://dx.doi.org/10.1002/pmic.201600470 10.1002/pmic.201600470]; GPMDB: [http://gpmdb.org/data/keyword/28464451 32]. | ||
#van Aalderen MC, van den Biggelaar M, Remmerswaal EBM, van Alphen FPJ, Meijer AB, Ten Berge IJM, van Lier RAW, (2017) "Label-free Analysis of CD8<sup>+</sup> T Cell Subset Proteomes Supports a Progressive Differentiation Model of Human-Virus-Specific T Cells." <i>Cell Rep</i> <b>19</b>(5):1068–1079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28467900 28467900]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.04.014 10.1016/j.celrep.2017.04.014]; GPMDB: [http://gpmdb.org/data/keyword/28467900 84]. | #van Aalderen MC, van den Biggelaar M, Remmerswaal EBM, van Alphen FPJ, Meijer AB, Ten Berge IJM, van Lier RAW, (2017) "Label-free Analysis of CD8<sup>+</sup> T Cell Subset Proteomes Supports a Progressive Differentiation Model of Human-Virus-Specific T Cells." <i>Cell Rep</i> <b>19</b>(5):1068–1079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28467900 28467900]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.04.014 10.1016/j.celrep.2017.04.014]; GPMDB: [http://gpmdb.org/data/keyword/28467900 84]. | ||
- | #Ozdian T, Holub D, Maceckova Z, Varanasi L, Rylova G, Rehulka J, Vaclavkova J, Slavik H, Moudry P, Znojek P, Stankova J, de Sanctis JB, Hajduch M, Dzubak P, (2017) "Proteomic profiling reveals DNA damage, nucleolar and ribosomal stress are the main responses to oxaliplatin treatment in cancer cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28478306 28478306]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.05.005 10.1016/j.jprot.2017.05.005]; GPMDB: [http://gpmdb.org/data/keyword/28478306 | + | #Tello-Lafoz M, Martínez-Martínez G, Rodríguez-Rodríguez C, Albar JP, Huse M, Gharbi S, Merida I, (2017) "SNX27 interactome in T lymphocytes identifies ZO-2 dynamic redistribution at the immune synapse." <i>Traffic</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28477369 28477369]; doi: [https://dx.doi.org/10.1111/tra.12492 10.1111/tra.12492]; GPMDB: [http://gpmdb.org/data/keyword/28477369 57]. |
+ | #Ozdian T, Holub D, Maceckova Z, Varanasi L, Rylova G, Rehulka J, Vaclavkova J, Slavik H, Moudry P, Znojek P, Stankova J, de Sanctis JB, Hajduch M, Dzubak P, (2017) "Proteomic profiling reveals DNA damage, nucleolar and ribosomal stress are the main responses to oxaliplatin treatment in cancer cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28478306 28478306]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.05.005 10.1016/j.jprot.2017.05.005]; GPMDB: [http://gpmdb.org/data/keyword/28478306 63]. | ||
#Murr A, Pink C, Hammer E, Michalik S, Dhople VM, Holtfreter B, Völker U, Kocher T, Gesell Salazar M, (2017) "Cross-Sectional Association of Salivary Proteins with Age, Sex, Body Mass Index, Smoking, and Education." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28481548 28481548]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00133 10.1021/acs.jproteome.7b00133]; GPMDB: [http://gpmdb.org/data/keyword/28481548 209]. | #Murr A, Pink C, Hammer E, Michalik S, Dhople VM, Holtfreter B, Völker U, Kocher T, Gesell Salazar M, (2017) "Cross-Sectional Association of Salivary Proteins with Age, Sex, Body Mass Index, Smoking, and Education." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28481548 28481548]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00133 10.1021/acs.jproteome.7b00133]; GPMDB: [http://gpmdb.org/data/keyword/28481548 209]. | ||
- | #Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ, (2017) "Common genetic variation drives molecular heterogeneity in human iPSCs." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28489815 28489815]; doi: [https://dx.doi.org/10.1038/nature22403 10.1038/nature22403]; GPMDB: [http://gpmdb.org/data/keyword/28489815 | + | #Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ, (2017) "Common genetic variation drives molecular heterogeneity in human iPSCs." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28489815 28489815]; doi: [https://dx.doi.org/10.1038/nature22403 10.1038/nature22403]; GPMDB: [http://gpmdb.org/data/keyword/28489815 72]. |
+ | #Kramer DA, Eldeeb MA, Wuest M, Mercer J, Fahlman RP, (2017) "Proteomic characterization of EL4 lymphoma derived tumors upon chemotherapy treatment reveals potential roles for lysosomes and caspase-6 during tumor cell death in vivo." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28508578 28508578]; doi: [https://dx.doi.org/10.1002/pmic.201700060 10.1002/pmic.201700060]; GPMDB: [http://gpmdb.org/data/keyword/28508578 66]. |
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 June 4, 2017.