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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 | + | 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 September 1, 2019. |
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T, (2018) "N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30150368 30150368]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000982 10.1074/mcp.RA118.000982]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30150368 17]. | #Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T, (2018) "N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30150368 30150368]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000982 10.1074/mcp.RA118.000982]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30150368 17]. | ||
#Béguin EP, van den Eshof BL, Hoogendijk AJ, Nota B, Mertens K, Meijer AB, van den Biggelaar M, (2018) "Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30153514 30153514]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.08.011 10.1016/j.jprot.2018.08.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30153514 51]. | #Béguin EP, van den Eshof BL, Hoogendijk AJ, Nota B, Mertens K, Meijer AB, van den Biggelaar M, (2018) "Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30153514 30153514]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.08.011 10.1016/j.jprot.2018.08.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30153514 51]. | ||
- | #Yanovich G, Agmon H, Harel M, Sonnenblick A, Peretz T, Geiger T, (2018) "Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification." <i>Cancer Res</i> <b>78</b>(20):6001–6010; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30154156 30154156]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-18-1079 10.1158/0008-5472.CAN-18-1079]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30154156 | + | #Yanovich G, Agmon H, Harel M, Sonnenblick A, Peretz T, Geiger T, (2018) "Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification." <i>Cancer Res</i> <b>78</b>(20):6001–6010; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30154156 30154156]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-18-1079 10.1158/0008-5472.CAN-18-1079]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30154156 30]. |
#Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
#Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | ||
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#Schoor C, Brocke-Ahmadinejad N, Gieselmann V, Winter D, (2019) "Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics." <i>Proteomics</i> <b></b>:e1900057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31216117 31216117]; doi: [https://dx.doi.org/10.1002/pmic.201900057 10.1002/pmic.201900057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31216117 5]. | #Schoor C, Brocke-Ahmadinejad N, Gieselmann V, Winter D, (2019) "Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics." <i>Proteomics</i> <b></b>:e1900057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31216117 31216117]; doi: [https://dx.doi.org/10.1002/pmic.201900057 10.1002/pmic.201900057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31216117 5]. | ||
#Alriquet M, Martínez-Limón A, Hanspach G, Hengesbach M, Tartaglia GG, Calloni G, Vabulas RM, (2019) "Assembly of Proteins by Free RNA during the Early Phase of Proteostasis Stress." <i>J Proteome Res</i> <b>18</b>(7):2835–2847; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31244213 31244213]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00143 10.1021/acs.jproteome.9b00143]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31244213 12]. | #Alriquet M, Martínez-Limón A, Hanspach G, Hengesbach M, Tartaglia GG, Calloni G, Vabulas RM, (2019) "Assembly of Proteins by Free RNA during the Early Phase of Proteostasis Stress." <i>J Proteome Res</i> <b>18</b>(7):2835–2847; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31244213 31244213]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00143 10.1021/acs.jproteome.9b00143]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31244213 12]. | ||
+ | #Drabovich AP, Saraon P, Drabovich M, Karakosta T, Dimitromanolakis A, Hyndman ME, Jarvi K, Diamandis EP, (2019) "Multi-omics biomarker pipeline reveals elevated levels of protein-glutamine gamma-glutamyltransferase 4 in seminal plasma of prostate cancer patients." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31249104 31249104]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001612 10.1074/mcp.RA119.001612]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31249104 10]. | ||
#Lignitto L, LeBoeuf SE, Homer H, Jiang S, Askenazi M, Karakousi TR, Pass HI, Bhutkar AJ, Tsirigos A, Ueberheide B, Sayin VI, Papagiannakopoulos T, Pagano M, (2019) "Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1." <i>Cell</i> <b>178</b>(2):316–329.e18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31257023 31257023]; doi: [https://dx.doi.org/10.1016/j.cell.2019.06.003 10.1016/j.cell.2019.06.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31257023 1]. | #Lignitto L, LeBoeuf SE, Homer H, Jiang S, Askenazi M, Karakousi TR, Pass HI, Bhutkar AJ, Tsirigos A, Ueberheide B, Sayin VI, Papagiannakopoulos T, Pagano M, (2019) "Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1." <i>Cell</i> <b>178</b>(2):316–329.e18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31257023 31257023]; doi: [https://dx.doi.org/10.1016/j.cell.2019.06.003 10.1016/j.cell.2019.06.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31257023 1]. | ||
#Holthenrich A, Drexler HCA, Chehab T, Naß J, Gerke V, (2019) "Proximity proteomics of endothelial Weibel-Palade bodies identifies novel regulator of von-Willebrand factor secretion." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31262780 31262780]; doi: [https://dx.doi.org/10.1182/blood.2019000786 10.1182/blood.2019000786]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31262780 12]. | #Holthenrich A, Drexler HCA, Chehab T, Naß J, Gerke V, (2019) "Proximity proteomics of endothelial Weibel-Palade bodies identifies novel regulator of von-Willebrand factor secretion." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31262780 31262780]; doi: [https://dx.doi.org/10.1182/blood.2019000786 10.1182/blood.2019000786]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31262780 12]. | ||
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#Gomig THB, Cavalli IJ, Souza RLR, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, Urban CA, Cavalli LR, Ribeiro EMSF, (2019) "High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data." <i>Data Brief</i> <b>25</b>:104125; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31294064 31294064]; doi: [https://dx.doi.org/10.1016/j.dib.2019.104125 10.1016/j.dib.2019.104125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31294064 69]. | #Gomig THB, Cavalli IJ, Souza RLR, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, Urban CA, Cavalli LR, Ribeiro EMSF, (2019) "High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data." <i>Data Brief</i> <b>25</b>:104125; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31294064 31294064]; doi: [https://dx.doi.org/10.1016/j.dib.2019.104125 10.1016/j.dib.2019.104125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31294064 69]. | ||
#Christakopoulos C, Cehofski LJ, Christensen SR, Vorum H, Honoré B, (2019) "Proteomics reveals a set of highly enriched proteins in epiretinal membrane compared with inner limiting membrane." <i>Exp Eye Res</i> <b>186</b>:107722; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31302158 31302158]; doi: [https://dx.doi.org/10.1016/j.exer.2019.107722 10.1016/j.exer.2019.107722]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31302158 71]. | #Christakopoulos C, Cehofski LJ, Christensen SR, Vorum H, Honoré B, (2019) "Proteomics reveals a set of highly enriched proteins in epiretinal membrane compared with inner limiting membrane." <i>Exp Eye Res</i> <b>186</b>:107722; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31302158 31302158]; doi: [https://dx.doi.org/10.1016/j.exer.2019.107722 10.1016/j.exer.2019.107722]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31302158 71]. | ||
+ | #Hsu CW, Chang KP, Huang Y, Liu HP, Hsueh PC, Gu PW, Yen WC, Wu CC, (2019) "Proteomic profiling of paired interstitial fluids reveals dysregulated pathways and salivary NID1 as a biomarker of oral cavity squamous cell carcinoma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31315917 31315917]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001654 10.1074/mcp.RA119.001654]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31315917 900]. | ||
#Kang T, Boland BB, Alarcon C, Grimsby JS, Rhodes CJ, Larsen MR, (2019) "Proteomic Analysis of Restored Insulin Production and Trafficking in Obese Diabetic Mouse Pancreatic Islets Following Euglycemia." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31317746 31317746]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00160 10.1021/acs.jproteome.9b00160]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31317746 66]. | #Kang T, Boland BB, Alarcon C, Grimsby JS, Rhodes CJ, Larsen MR, (2019) "Proteomic Analysis of Restored Insulin Production and Trafficking in Obese Diabetic Mouse Pancreatic Islets Following Euglycemia." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31317746 31317746]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00160 10.1021/acs.jproteome.9b00160]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31317746 66]. | ||
#Patil S, Rajagopalan P, Patel K, Subbannayya T, Babu N, Mohan SV, Advani J, Sathe G, Bhandi S, Solanki HS, Sidransky D, Chatterjee A, Gowda H, Ferrari M, (2019) "Chronic shisha exposure alters phosphoproteome of oral keratinocytes." <i>J Cell Commun Signal</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31321732 31321732]; doi: [https://dx.doi.org/10.1007/s12079-019-00528-4 10.1007/s12079-019-00528-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31321732 6]. | #Patil S, Rajagopalan P, Patel K, Subbannayya T, Babu N, Mohan SV, Advani J, Sathe G, Bhandi S, Solanki HS, Sidransky D, Chatterjee A, Gowda H, Ferrari M, (2019) "Chronic shisha exposure alters phosphoproteome of oral keratinocytes." <i>J Cell Commun Signal</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31321732 31321732]; doi: [https://dx.doi.org/10.1007/s12079-019-00528-4 10.1007/s12079-019-00528-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31321732 6]. | ||
- | #Buser DP, Ritz MF, Moes S, Tostado C, Frank S, Spiess M, Mariani L, Jenö P, Boulay JL, Hutter G, (2019) "Quantitative proteomics reveals reduction of endocytic machinery components in gliomas." <i>EBioMedicine</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31331834 31331834]; doi: [https://dx.doi.org/10.1016/j.ebiom.2019.07.039 10.1016/j.ebiom.2019.07.039]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31331834 | + | #Buser DP, Ritz MF, Moes S, Tostado C, Frank S, Spiess M, Mariani L, Jenö P, Boulay JL, Hutter G, (2019) "Quantitative proteomics reveals reduction of endocytic machinery components in gliomas." <i>EBioMedicine</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31331834 31331834]; doi: [https://dx.doi.org/10.1016/j.ebiom.2019.07.039 10.1016/j.ebiom.2019.07.039]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31331834 51]. |
+ | #Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS, (2019) "Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality." <i>Cell Rep</i> <b>28</b>(6):1635–1647.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31390575 31390575]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.07.019 10.1016/j.celrep.2019.07.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31390575 723]. |
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 September 1, 2019.