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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 July | + | 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 29, 2018. |
#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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#Lim S, Kim D, Ju S, Shin S, Cho IJ, Park SH, Grailhe R, Lee C, Kim YK, (2018) "Glioblastoma-secreted soluble CD44 activates tau pathology in the brain." <i>Exp Mol Med</i> <b>50</b>(4):5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29622771 29622771]; doi: [https://dx.doi.org/10.1038/s12276-017-0008-7 10.1038/s12276-017-0008-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29622771 2]. | #Lim S, Kim D, Ju S, Shin S, Cho IJ, Park SH, Grailhe R, Lee C, Kim YK, (2018) "Glioblastoma-secreted soluble CD44 activates tau pathology in the brain." <i>Exp Mol Med</i> <b>50</b>(4):5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29622771 29622771]; doi: [https://dx.doi.org/10.1038/s12276-017-0008-7 10.1038/s12276-017-0008-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29622771 2]. | ||
#Sanz-Bravo A, Alvarez-Navarro C, Martín-Esteban A, Barnea E, Admon A, López de Castro JA, (2018) "Ranking the contribution of ankylosing spondylitis-associated ERAP1 polymorphisms to shaping the HLA-B*27 peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29632046 29632046]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000565 10.1074/mcp.RA117.000565]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29632046 15]. | #Sanz-Bravo A, Alvarez-Navarro C, Martín-Esteban A, Barnea E, Admon A, López de Castro JA, (2018) "Ranking the contribution of ankylosing spondylitis-associated ERAP1 polymorphisms to shaping the HLA-B*27 peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29632046 29632046]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000565 10.1074/mcp.RA117.000565]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29632046 15]. | ||
+ | #Wu W, Zaal EA, Berkers CR, Lemeer S, Heck AJR, (2018) "CTGF/VEGFA-activated fibroblasts promote tumor migration through micro-environmental modulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29669735 29669735]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000708 10.1074/mcp.RA118.000708]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29669735 57]. | ||
#Johnston D, Malo Estepa I, Ebhardt HA, Crowe MA, Diskin MG, (2018) "Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle." <i>Theriogenology</i> <b>114</b>:301–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29677633 29677633]; doi: [https://dx.doi.org/10.1016/j.theriogenology.2018.04.008 10.1016/j.theriogenology.2018.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29677633 63]. | #Johnston D, Malo Estepa I, Ebhardt HA, Crowe MA, Diskin MG, (2018) "Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle." <i>Theriogenology</i> <b>114</b>:301–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29677633 29677633]; doi: [https://dx.doi.org/10.1016/j.theriogenology.2018.04.008 10.1016/j.theriogenology.2018.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29677633 63]. | ||
#Komov L, Kadosh DM, Barnea E, Milner E, Hendler A, Admon A, (2018) "Cell Surface MHC Class I Expression is Limited by the Availability of Peptide-Receptive 'Empty' Molecules Rather than by the Supply of Peptide Ligands." <i>Proteomics</i> <b></b>:e1700248; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707912 29707912]; doi: [https://dx.doi.org/10.1002/pmic.201700248 10.1002/pmic.201700248]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707912 35]. | #Komov L, Kadosh DM, Barnea E, Milner E, Hendler A, Admon A, (2018) "Cell Surface MHC Class I Expression is Limited by the Availability of Peptide-Receptive 'Empty' Molecules Rather than by the Supply of Peptide Ligands." <i>Proteomics</i> <b></b>:e1700248; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707912 29707912]; doi: [https://dx.doi.org/10.1002/pmic.201700248 10.1002/pmic.201700248]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707912 35]. | ||
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#Rapino F, Delaunay S, Rambow F, Zhou Z, Tharun L, De Tullio P, Sin O, Shostak K, Schmitz S, Piepers J, Ghesquière B, Karim L, Charloteaux B, Jamart D, Florin A, Lambert C, Rorive A, Jerusalem G, Leucci E, Dewaele M, Vooijs M, Leidel SA, Georges M, Voz M, Peers B, Büttner R, Marine JC, Chariot A, Close P, (2018) "Codon-specific translation reprogramming promotes resistance to targeted therapy." <i>Nature</i> <b>558</b>(7711):605–609; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29925953 29925953]; doi: [https://dx.doi.org/10.1038/s41586-018-0243-7 10.1038/s41586-018-0243-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29925953 40]. | #Rapino F, Delaunay S, Rambow F, Zhou Z, Tharun L, De Tullio P, Sin O, Shostak K, Schmitz S, Piepers J, Ghesquière B, Karim L, Charloteaux B, Jamart D, Florin A, Lambert C, Rorive A, Jerusalem G, Leucci E, Dewaele M, Vooijs M, Leidel SA, Georges M, Voz M, Peers B, Büttner R, Marine JC, Chariot A, Close P, (2018) "Codon-specific translation reprogramming promotes resistance to targeted therapy." <i>Nature</i> <b>558</b>(7711):605–609; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29925953 29925953]; doi: [https://dx.doi.org/10.1038/s41586-018-0243-7 10.1038/s41586-018-0243-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29925953 40]. | ||
#Kim DS, Anantharam P, Hoffmann A, Meade ML, Grobe N, Gearhart JM, Whitley EM, Mahama B, Rumbeiha WK, (2018) "Broad spectrum proteomics analysis of the inferior colliculus following acute hydrogen sulfide exposure." <i>Toxicol Appl Pharmacol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29932956 29932956]; doi: [https://dx.doi.org/10.1016/j.taap.2018.06.001 10.1016/j.taap.2018.06.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29932956 6]. | #Kim DS, Anantharam P, Hoffmann A, Meade ML, Grobe N, Gearhart JM, Whitley EM, Mahama B, Rumbeiha WK, (2018) "Broad spectrum proteomics analysis of the inferior colliculus following acute hydrogen sulfide exposure." <i>Toxicol Appl Pharmacol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29932956 29932956]; doi: [https://dx.doi.org/10.1016/j.taap.2018.06.001 10.1016/j.taap.2018.06.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29932956 6]. | ||
- | #Zhu Y, Dou M, Piehowski PD, Liang Y, Wang F, Chu RK, Chrisler W, Smith JN, Schwarz KC, Shen Y, Shukla AK, Moore RJ, Smith RD, Qian WJ, Kelly RT, (2018) "Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29941660 29941660]; doi: [https://dx.doi.org/10.1074/mcp.TIR118.000686 10.1074/mcp.TIR118.000686]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29941660 | + | #Zhu Y, Dou M, Piehowski PD, Liang Y, Wang F, Chu RK, Chrisler W, Smith JN, Schwarz KC, Shen Y, Shukla AK, Moore RJ, Smith RD, Qian WJ, Kelly RT, (2018) "Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29941660 29941660]; doi: [https://dx.doi.org/10.1074/mcp.TIR118.000686 10.1074/mcp.TIR118.000686]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29941660 24]. |
#Drulis-Fajdasz D, Rakus D, Wiśniewski JR, McCubrey JA, Gizak A, (2018) "Systematic analysis of GSK-3 signaling pathways in aging of cerebral tissue." <i>Adv Biol Regul</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29958836 29958836]; doi: [https://dx.doi.org/10.1016/j.jbior.2018.06.001 10.1016/j.jbior.2018.06.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29958836 72]. | #Drulis-Fajdasz D, Rakus D, Wiśniewski JR, McCubrey JA, Gizak A, (2018) "Systematic analysis of GSK-3 signaling pathways in aging of cerebral tissue." <i>Adv Biol Regul</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29958836 29958836]; doi: [https://dx.doi.org/10.1016/j.jbior.2018.06.001 10.1016/j.jbior.2018.06.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29958836 72]. | ||
#Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ, (2018) "Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria." <i>Nat Commun</i> <b>9</b>(1):2558; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967381 29967381]; doi: [https://dx.doi.org/10.1038/s41467-018-05007-9 10.1038/s41467-018-05007-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967381 18]. | #Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ, (2018) "Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria." <i>Nat Commun</i> <b>9</b>(1):2558; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967381 29967381]; doi: [https://dx.doi.org/10.1038/s41467-018-05007-9 10.1038/s41467-018-05007-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967381 18]. | ||
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#Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK, (2018) "Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells - Transmission of hallmarks of nuclear organization through mitosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29991507 29991507]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000591 10.1074/mcp.RA118.000591]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29991507 6]. | #Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK, (2018) "Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells - Transmission of hallmarks of nuclear organization through mitosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29991507 29991507]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000591 10.1074/mcp.RA118.000591]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29991507 6]. | ||
#Kim D, Liu Y, Oberly S, Freire R, Smolka MB, (2018) "ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30010936 30010936]; doi: [https://dx.doi.org/10.1093/nar/gky625 10.1093/nar/gky625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30010936 2]. | #Kim D, Liu Y, Oberly S, Freire R, Smolka MB, (2018) "ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30010936 30010936]; doi: [https://dx.doi.org/10.1093/nar/gky625 10.1093/nar/gky625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30010936 2]. | ||
+ | #Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR, (2018) "53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30046110 30046110]; doi: [https://dx.doi.org/10.1038/s41586-018-0362-1 10.1038/s41586-018-0362-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30046110 8]. |
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 29, 2018.