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#Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J, (2015) "Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome." <i>Sci Rep</i> <b>5</b>:18019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26658305 26658305]; doi: [https://dx.doi.org/10.1038/srep18019 10.1038/srep18019]; GPMDB: [http://gpmdb.org/data/keyword/26658305 36]. | #Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J, (2015) "Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome." <i>Sci Rep</i> <b>5</b>:18019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26658305 26658305]; doi: [https://dx.doi.org/10.1038/srep18019 10.1038/srep18019]; GPMDB: [http://gpmdb.org/data/keyword/26658305 36]. | ||
#Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S, (2015) "Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction." <i>Microbiologyopen</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26663479 26663479]; doi: [https://dx.doi.org/10.1002/mbo3.320 10.1002/mbo3.320]; GPMDB: [http://gpmdb.org/data/keyword/26663479 10]. | #Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S, (2015) "Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction." <i>Microbiologyopen</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26663479 26663479]; doi: [https://dx.doi.org/10.1002/mbo3.320 10.1002/mbo3.320]; GPMDB: [http://gpmdb.org/data/keyword/26663479 10]. | ||
+ | #Ulaganathan VK, Sperl B, Rapp UR, Ullrich A, (2015) "Germline variant FGFR4 p.G388R exposes a membrane-proximal STAT3 binding site." <i>Nature</i> <b>528</b>(7583):570–4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26675719 26675719]; doi: [https://dx.doi.org/10.1038/nature16449 10.1038/nature16449]; GPMDB: [http://gpmdb.org/data/keyword/26675719 32]. | ||
#Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC, (2015) "The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26682798 26682798]; doi: [https://dx.doi.org/10.1093/nar/gkv1473 10.1093/nar/gkv1473]; GPMDB: [http://gpmdb.org/data/keyword/26682798 4]. | #Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC, (2015) "The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26682798 26682798]; doi: [https://dx.doi.org/10.1093/nar/gkv1473 10.1093/nar/gkv1473]; GPMDB: [http://gpmdb.org/data/keyword/26682798 4]. | ||
#Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ, (2015) "Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries." <i>Microbiome</i> <b>3</b>(1):69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26684897 26684897]; doi: [https://dx.doi.org/10.1186/s40168-015-0136-z 10.1186/s40168-015-0136-z]; GPMDB: [http://gpmdb.org/data/keyword/26684897 24]. | #Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ, (2015) "Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries." <i>Microbiome</i> <b>3</b>(1):69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26684897 26684897]; doi: [https://dx.doi.org/10.1186/s40168-015-0136-z 10.1186/s40168-015-0136-z]; GPMDB: [http://gpmdb.org/data/keyword/26684897 24]. | ||
#Debaisieux S, Encheva V, Chakravarty P, Snijders AP, Schiavo G, (2015) "Analysis of signaling endosome composition and dynamics using SILAC in embryonic stem cell-derived neurons." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26685126 26685126]; doi: [https://dx.doi.org/10.1074/mcp.M115.051649 10.1074/mcp.M115.051649]; GPMDB: [http://gpmdb.org/data/keyword/26685126 28]. | #Debaisieux S, Encheva V, Chakravarty P, Snijders AP, Schiavo G, (2015) "Analysis of signaling endosome composition and dynamics using SILAC in embryonic stem cell-derived neurons." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26685126 26685126]; doi: [https://dx.doi.org/10.1074/mcp.M115.051649 10.1074/mcp.M115.051649]; GPMDB: [http://gpmdb.org/data/keyword/26685126 28]. | ||
- | #Oberbach A, Adams V, Schlichting N, Heinrich M, Kullnick Y, Lehmann S, Lehmann S, Feder S, Correia JC, Mohr FW, Völker U, Jehmlich N, ( | + | #Oberbach A, Adams V, Schlichting N, Heinrich M, Kullnick Y, Lehmann S, Lehmann S, Feder S, Correia JC, Mohr FW, Völker U, Jehmlich N, (2016) "Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins." <i>Clin Chim Acta</i> <b>453</b>:114–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26688386 26688386]; doi: [https://dx.doi.org/10.1016/j.cca.2015.12.005 10.1016/j.cca.2015.12.005]; GPMDB: [http://gpmdb.org/data/keyword/26688386 10]. |
#Eitzinger N, Wagner V, Weisheit W, Geimer S, Boness D, Kreimer G, Mittag M, (2015) "Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation." <i>Front Plant Sci</i> <b>6</b>:1085; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26697039 26697039]; doi: [https://dx.doi.org/10.3389/fpls.2015.01085 10.3389/fpls.2015.01085]; GPMDB: [http://gpmdb.org/data/keyword/26697039 128]. | #Eitzinger N, Wagner V, Weisheit W, Geimer S, Boness D, Kreimer G, Mittag M, (2015) "Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation." <i>Front Plant Sci</i> <b>6</b>:1085; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26697039 26697039]; doi: [https://dx.doi.org/10.3389/fpls.2015.01085 10.3389/fpls.2015.01085]; GPMDB: [http://gpmdb.org/data/keyword/26697039 128]. | ||
#Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin MF, (2015) "ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26699800 26699800]; doi: [https://dx.doi.org/10.1074/mcp.M115.055723 10.1074/mcp.M115.055723]; GPMDB: [http://gpmdb.org/data/keyword/26699800 141]. | #Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin MF, (2015) "ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26699800 26699800]; doi: [https://dx.doi.org/10.1074/mcp.M115.055723 10.1074/mcp.M115.055723]; GPMDB: [http://gpmdb.org/data/keyword/26699800 141]. | ||
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#Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Mueller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G, (2015) "An inducible retroviral expression system for tandem affinity purification mass-spectrometry-based proteomics identifies MLKL as an HSP90 client." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26714523 26714523]; doi: [https://dx.doi.org/10.1074/mcp.O115.055350 10.1074/mcp.O115.055350]; GPMDB: [http://gpmdb.org/data/keyword/26714523 16]. | #Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Mueller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G, (2015) "An inducible retroviral expression system for tandem affinity purification mass-spectrometry-based proteomics identifies MLKL as an HSP90 client." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26714523 26714523]; doi: [https://dx.doi.org/10.1074/mcp.O115.055350 10.1074/mcp.O115.055350]; GPMDB: [http://gpmdb.org/data/keyword/26714523 16]. | ||
#Bode D, Yu L, Tate P, Pardo M, Choudhary JS, (2015) "Characterisation of two distinct Nucleosome Remodelling and Deacetylase Complex (NuRD) assemblies in embryonic stem cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26714524 26714524]; doi: [https://dx.doi.org/10.1074/mcp.M115.053207 10.1074/mcp.M115.053207]; GPMDB: [http://gpmdb.org/data/keyword/26714524 179]. | #Bode D, Yu L, Tate P, Pardo M, Choudhary JS, (2015) "Characterisation of two distinct Nucleosome Remodelling and Deacetylase Complex (NuRD) assemblies in embryonic stem cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26714524 26714524]; doi: [https://dx.doi.org/10.1074/mcp.M115.053207 10.1074/mcp.M115.053207]; GPMDB: [http://gpmdb.org/data/keyword/26714524 179]. | ||
- | #Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV, ( | + | #McAfee A, Harpur BA, Michaud S, Beavis RC, Kent CF, Zayed A, Foster LJ, (2016) "Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26718741 26718741]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00589 10.1021/acs.jproteome.5b00589]; GPMDB: [http://gpmdb.org/data/keyword/26718741 27]. |
+ | #Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV, (2016) "Protein turnover during in vitro tissue engineering." <i>Biomaterials</i> <b>81</b>:104–13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26724458 26724458]; doi: [https://dx.doi.org/10.1016/j.biomaterials.2015.12.004 10.1016/j.biomaterials.2015.12.004]; GPMDB: [http://gpmdb.org/data/keyword/26724458 66]. | ||
#Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, (2016) "Proteomic maps of breast cancer subtypes." <i>Nat Commun</i> <b>7</b>:10259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26725330 26725330]; doi: [https://dx.doi.org/10.1038/ncomms10259 10.1038/ncomms10259]; GPMDB: [http://gpmdb.org/data/keyword/26725330 255]. | #Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, (2016) "Proteomic maps of breast cancer subtypes." <i>Nat Commun</i> <b>7</b>:10259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26725330 26725330]; doi: [https://dx.doi.org/10.1038/ncomms10259 10.1038/ncomms10259]; GPMDB: [http://gpmdb.org/data/keyword/26725330 255]. | ||
#Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, (2016) "DCAF1 controls T-cell function via p53-dependent and -independent mechanisms." <i>Nat Commun</i> <b>7</b>:10307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728942 26728942]; doi: [https://dx.doi.org/10.1038/ncomms10307 10.1038/ncomms10307]; GPMDB: [http://gpmdb.org/data/keyword/26728942 120]. | #Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, (2016) "DCAF1 controls T-cell function via p53-dependent and -independent mechanisms." <i>Nat Commun</i> <b>7</b>:10307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728942 26728942]; doi: [https://dx.doi.org/10.1038/ncomms10307 10.1038/ncomms10307]; GPMDB: [http://gpmdb.org/data/keyword/26728942 120]. | ||
#Clark DJ, Fondrie WE, Yang A, Mao L, (2015) "Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26739763 26739763]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.12.023 10.1016/j.jprot.2015.12.023]; GPMDB: [http://gpmdb.org/data/keyword/26739763 3]. | #Clark DJ, Fondrie WE, Yang A, Mao L, (2015) "Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26739763 26739763]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.12.023 10.1016/j.jprot.2015.12.023]; GPMDB: [http://gpmdb.org/data/keyword/26739763 3]. | ||
+ | #Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [http://gpmdb.org/data/keyword/26745281 72]. | ||
+ | #Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Arias AM, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:9992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [http://gpmdb.org/data/keyword/26754106 2]. | ||
+ | #Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Colwill K, Pawson T, (2016) "Mutational analysis of GSK3β protein kinase together with kinome-wide binding and stability studies suggest context-dependent recognition of kinases by the chaperone HSP90." <i>Mol Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755559 26755559]; doi: [https://dx.doi.org/10.1128/MCB.01045-15 10.1128/MCB.01045-15]; GPMDB: [http://gpmdb.org/data/keyword/26755559 17]. | ||
+ | #Geddes JM, Caza M, Croll D, Stoynov N, Foster LJ, Kronstad JW, (2016) "Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation." <i>MBio</i> <b>7</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26758180 26758180]; doi: [https://dx.doi.org/10.1128/mBio.01862-15 10.1128/mBio.01862-15]; GPMDB: [http://gpmdb.org/data/keyword/26758180 133]. | ||
+ | #Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen IS, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S, (2016) "Mapping the O-mannose glycoproteome in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26764011 26764011]; doi: [https://dx.doi.org/10.1074/mcp.M115.057505 10.1074/mcp.M115.057505]; GPMDB: [http://gpmdb.org/data/keyword/26764011 6]. | ||
+ | #Kümper S, Mardakheh FK, McCarthy A, Yeo M, Stamp GW, Paul A, Worboys J, Sadok A, Jørgensen C, Guichard S, Marshall CJ, (2016) "Rho-associated kinase (ROCK) function is essential for cell cycle progression, senescence and tumorigenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26765561 26765561]; doi: [https://dx.doi.org/10.7554/eLife.12203 10.7554/eLife.12203]; GPMDB: [http://gpmdb.org/data/keyword/26765561 28]. |
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 pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a 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 17, 2016.