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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. | 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. | ||
- | <b>CAUTION</b>: Many papers contain serious errors in their | + | <b>CAUTION</b>:Many datasets/papers contain serious errors in their metadata/methods sections. When using data from repositories, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methods, etc.) that may impact on your use of the data. We have corrected for as many of these errors as we could detect, but there is no way to be sure that we found them all. When attempting to analyze or reproduce results, keep in mind the likelihood that key parts of the experimental methods may have been recorded incorrectly in the associated metadata or manuscript. |
==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 January 1, 2024. |
#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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#Steiner G, Marban-Doran C, Langer J, Pimenova T, Duran-Pacheco G, Sauter D, Langenkamp A, Solier C, Singer T, Bray-French K, Ducret A, (2020) "Enabling Routine MHC-II-Associated Peptide Proteomics for Risk Assessment of Drug-Induced Immunogenicity." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32786679 32786679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00309 10.1021/acs.jproteome.0c00309]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32786679 162]. | #Steiner G, Marban-Doran C, Langer J, Pimenova T, Duran-Pacheco G, Sauter D, Langenkamp A, Solier C, Singer T, Bray-French K, Ducret A, (2020) "Enabling Routine MHC-II-Associated Peptide Proteomics for Risk Assessment of Drug-Induced Immunogenicity." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32786679 32786679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00309 10.1021/acs.jproteome.0c00309]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32786679 162]. | ||
#Kirak O, Ke E, Yang KY, Schwarz A, Plate L, Nham A, Abadejos JR, Valencia A, Wiseman RL, Lui KO, Ku M, (2020) "Premature Activation of Immune Transcription Programs in Autoimmune-Predisposed Mouse Embryonic Stem Cells and Blastocysts." <i>Int J Mol Sci</i> <b>21</b>(16):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32796510 32796510]; doi: [https://dx.doi.org/10.3390/ijms21165743 10.3390/ijms21165743]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32796510 1]. | #Kirak O, Ke E, Yang KY, Schwarz A, Plate L, Nham A, Abadejos JR, Valencia A, Wiseman RL, Lui KO, Ku M, (2020) "Premature Activation of Immune Transcription Programs in Autoimmune-Predisposed Mouse Embryonic Stem Cells and Blastocysts." <i>Int J Mol Sci</i> <b>21</b>(16):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32796510 32796510]; doi: [https://dx.doi.org/10.3390/ijms21165743 10.3390/ijms21165743]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32796510 1]. | ||
+ | #Leng L, Cao R, Ma J, Mou D, Zhu Y, Li W, Lv L, Gao D, Zhang S, Gong F, Zhao L, Qiu B, Xiang H, Hu Z, Feng Y, Dai Y, Zhao J, Wu Z, Li H, Zhong W, (2020) "Pathological features of COVID-19-associated lung injury: a preliminary proteomics report based on clinical samples." <i>Signal Transduct Target Ther</i> <b>5</b>(1):240; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33060566 33060566]; doi: [https://dx.doi.org/10.1038/s41392-020-00355-9 10.1038/s41392-020-00355-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33060566 13]. | ||
+ | #Tijms BM, Gobom J, Reus L, Jansen I, Hong S, Dobricic V, Kilpert F, Ten Kate M, Barkhof F, Tsolaki M, Verhey FRJ, Popp J, Martinez-Lage P, Vandenberghe R, Lleó A, Molinuevo JL, Engelborghs S, Bertram L, Lovestone S, Streffer J, Vos S, Bos I, Alzheimer’s Disease Neuroimaging Initiative (ADNI)., Blennow K, Scheltens P, Teunissen CE, Zetterberg H, Visser PJ, (2020) "Pathophysiological subtypes of Alzheimer's disease based on cerebrospinal fluid proteomics." <i>Brain</i> <b>143</b>(12):3776–3792; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33439986 33439986]; doi: [https://dx.doi.org/10.1093/brain/awaa325 10.1093/brain/awaa325]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33439986 36]. | ||
+ | #Lobato-Gil S, Heidelberger JB, Maghames C, Bailly A, Brunello L, Rodriguez MS, Beli P, Xirodimas DP, (2021) "Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation." <i>Cell Rep</i> <b>34</b>(3):108635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33472076 33472076]; doi: [https://dx.doi.org/10.1016/j.celrep.2020.108635 10.1016/j.celrep.2020.108635]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33472076 24]. | ||
+ | #Del Favero G, Janker L, Neuditschko B, Hohenbichler J, Kiss E, Woelflingseder L, Gerner C, Marko D, (2021) "Exploring the dermotoxicity of the mycotoxin deoxynivalenol: combined morphologic and proteomic profiling of human epidermal cells reveals alteration of lipid biosynthesis machinery and membrane structural integrity relevant for skin barrier function." <i>Arch Toxicol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33890134 33890134]; doi: [https://dx.doi.org/10.1007/s00204-021-03042-y 10.1007/s00204-021-03042-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33890134 58]. |
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 datasets/papers contain serious errors in their metadata/methods sections. When using data from repositories, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methods, etc.) that may impact on your use of the data. We have corrected for as many of these errors as we could detect, but there is no way to be sure that we found them all. When attempting to analyze or reproduce results, keep in mind the likelihood that key parts of the experimental methods may have been recorded incorrectly in the associated metadata or manuscript.
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 January 1, 2024.