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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 July 20, 2020. |
#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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#Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B, (2020) "Meltome atlas-thermal proteome stability across the tree of life." <i>Nat Methods</i> <b>17</b>(5):495–503; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32284610 32284610]; doi: [https://dx.doi.org/10.1038/s41592-020-0801-4 10.1038/s41592-020-0801-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32284610 31]. | #Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B, (2020) "Meltome atlas-thermal proteome stability across the tree of life." <i>Nat Methods</i> <b>17</b>(5):495–503; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32284610 32284610]; doi: [https://dx.doi.org/10.1038/s41592-020-0801-4 10.1038/s41592-020-0801-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32284610 31]. | ||
#Goebel T, Mausbach S, Tuermer A, Eltahir H, Winter D, Gieselmann V, Thelen M, (2020) "Proteaphagy in mammalian cells can function independent of ATG5/ATG7." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32299840 32299840]; doi: [https://dx.doi.org/10.1074/mcp.RA120.001983 10.1074/mcp.RA120.001983]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32299840 149]. | #Goebel T, Mausbach S, Tuermer A, Eltahir H, Winter D, Gieselmann V, Thelen M, (2020) "Proteaphagy in mammalian cells can function independent of ATG5/ATG7." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32299840 32299840]; doi: [https://dx.doi.org/10.1074/mcp.RA120.001983 10.1074/mcp.RA120.001983]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32299840 149]. | ||
+ | #Pancholi S, Ribas R, Simigdala N, Schuster E, Nikitorowicz-Buniak J, Ressa A, Gao Q, Leal MF, Bhamra A, Thornhill A, Morisset L, Montaudon E, Sourd L, Fitzpatrick M, Altelaar M, Johnston SR, Marangoni E, Dowsett M, Martin LA, (2020) "Tumour kinome re-wiring governs resistance to palbociclib in oestrogen receptor positive breast cancers, highlighting new therapeutic modalities." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32307447 32307447]; doi: [https://dx.doi.org/10.1038/s41388-020-1284-6 10.1038/s41388-020-1284-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32307447 36]. | ||
#Chen Z, Wang C, Lei C, Feng X, Li C, Jung SY, Qin J, Chen J, (2020) "Phosphoproteomics Analysis Reveals a Potential Role of CHK1 in Regulation of Innate Immunity through IRF3." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32314919 32314919]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00829 10.1021/acs.jproteome.9b00829]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32314919 48]. | #Chen Z, Wang C, Lei C, Feng X, Li C, Jung SY, Qin J, Chen J, (2020) "Phosphoproteomics Analysis Reveals a Potential Role of CHK1 in Regulation of Innate Immunity through IRF3." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32314919 32314919]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00829 10.1021/acs.jproteome.9b00829]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32314919 48]. | ||
#Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A, (2020) "BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain." <i>Cell Syst</i> <b>10</b>(4):333–350.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32325033 32325033]; doi: [https://dx.doi.org/10.1016/j.cels.2020.03.003 10.1016/j.cels.2020.03.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32325033 578]. | #Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A, (2020) "BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain." <i>Cell Syst</i> <b>10</b>(4):333–350.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32325033 32325033]; doi: [https://dx.doi.org/10.1016/j.cels.2020.03.003 10.1016/j.cels.2020.03.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32325033 578]. | ||
#Ojalill M, Virtanen N, Rappu P, Siljamäki E, Taimen P, Heino J, (2020) "Interaction between prostate cancer cells and prostate fibroblasts promotes accumulation and proteolytic processing of basement membrane proteins." <i>Prostate</i> <b>80</b>(9):715–726; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32364250 32364250]; doi: [https://dx.doi.org/10.1002/pros.23985 10.1002/pros.23985]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32364250 18]. | #Ojalill M, Virtanen N, Rappu P, Siljamäki E, Taimen P, Heino J, (2020) "Interaction between prostate cancer cells and prostate fibroblasts promotes accumulation and proteolytic processing of basement membrane proteins." <i>Prostate</i> <b>80</b>(9):715–726; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32364250 32364250]; doi: [https://dx.doi.org/10.1002/pros.23985 10.1002/pros.23985]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32364250 18]. | ||
#Bekes K, Mitulović G, Meißner N, Resch U, Gruber R, (2020) "Saliva proteomic patterns in patients with molar incisor hypomineralization." <i>Sci Rep</i> <b>10</b>(1):7560; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32371984 32371984]; doi: [https://dx.doi.org/10.1038/s41598-020-64614-z 10.1038/s41598-020-64614-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32371984 10]. | #Bekes K, Mitulović G, Meißner N, Resch U, Gruber R, (2020) "Saliva proteomic patterns in patients with molar incisor hypomineralization." <i>Sci Rep</i> <b>10</b>(1):7560; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32371984 32371984]; doi: [https://dx.doi.org/10.1038/s41598-020-64614-z 10.1038/s41598-020-64614-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32371984 10]. | ||
+ | #Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B, (2020) "Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32591346 32591346]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002164 10.1074/mcp.RA120.002164]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32591346 96]. |
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 July 20, 2020.