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#Portela M, Yang L, Paul S, Li X, Veraksa A, Parsons LM, Richardson HE, (2018) "Lgl reduces endosomal vesicle acidification and Notch signaling by promoting the interaction between Vap33 and the V-ATPase complex." <i>Sci Signal</i> <b>11</b>(533):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29871910 29871910]; doi: [https://dx.doi.org/10.1126/scisignal.aar1976 10.1126/scisignal.aar1976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29871910 11]. | #Portela M, Yang L, Paul S, Li X, Veraksa A, Parsons LM, Richardson HE, (2018) "Lgl reduces endosomal vesicle acidification and Notch signaling by promoting the interaction between Vap33 and the V-ATPase complex." <i>Sci Signal</i> <b>11</b>(533):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29871910 29871910]; doi: [https://dx.doi.org/10.1126/scisignal.aar1976 10.1126/scisignal.aar1976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29871910 11]. | ||
#Serandour AA, Mohammed H, Miremadi A, Mulder KW, Carroll JS, (2018) "TRPS1 regulates oestrogen receptor binding and histone acetylation at enhancers." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29895970 29895970]; doi: [https://dx.doi.org/10.1038/s41388-018-0312-2 10.1038/s41388-018-0312-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29895970 7]. | #Serandour AA, Mohammed H, Miremadi A, Mulder KW, Carroll JS, (2018) "TRPS1 regulates oestrogen receptor binding and histone acetylation at enhancers." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29895970 29895970]; doi: [https://dx.doi.org/10.1038/s41388-018-0312-2 10.1038/s41388-018-0312-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29895970 7]. | ||
- | #Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2018) "Time-course proteomics dataset to monitor protein-bound methionine oxidation <i>in Bacillus cereus</i> ATCC 14579." <i>Data Brief</i> <b>18</b>:394–398; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29896523 29896523]; doi: [https://dx.doi.org/10.1016/j.dib.2018.03.030 10.1016/j.dib.2018.03.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29896523 | + | #Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2018) "Time-course proteomics dataset to monitor protein-bound methionine oxidation <i>in Bacillus cereus</i> ATCC 14579." <i>Data Brief</i> <b>18</b>:394–398; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29896523 29896523]; doi: [https://dx.doi.org/10.1016/j.dib.2018.03.030 10.1016/j.dib.2018.03.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29896523 86]. |
#He C, Jia C, Zhang Y, Xu P, (2018) "Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29897761 29897761]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00032 10.1021/acs.jproteome.8b00032]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29897761 20]. | #He C, Jia C, Zhang Y, Xu P, (2018) "Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29897761 29897761]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00032 10.1021/acs.jproteome.8b00032]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29897761 20]. | ||
#Adav SS, Wei J, Terence Y, Ang BC, Yip LW, Sze SK, (2018) "Proteomic Analysis of Aqueous Humor from Primary Open Angle Glaucoma Patients on Drug Treatment Revealed Altered Complement Activation Cascade." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29901396 29901396]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00244 10.1021/acs.jproteome.8b00244]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29901396 80]. | #Adav SS, Wei J, Terence Y, Ang BC, Yip LW, Sze SK, (2018) "Proteomic Analysis of Aqueous Humor from Primary Open Angle Glaucoma Patients on Drug Treatment Revealed Altered Complement Activation Cascade." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29901396 29901396]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00244 10.1021/acs.jproteome.8b00244]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29901396 80]. | ||
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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 23]. | ||
#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]. | ||
#Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B, (2018) "UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites." <i>Nat Struct Mol Biol</i> <b>25</b>(7):631–640; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967540 29967540]; doi: [https://dx.doi.org/10.1038/s41594-018-0084-y 10.1038/s41594-018-0084-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967540 136]. | #Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B, (2018) "UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites." <i>Nat Struct Mol Biol</i> <b>25</b>(7):631–640; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967540 29967540]; doi: [https://dx.doi.org/10.1038/s41594-018-0084-y 10.1038/s41594-018-0084-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967540 136]. | ||
#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]. |
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 22, 2018.