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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 Oct. | + | 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 Oct. 29, 2017. |
#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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Schanzenbächer CT, Sambandan S, Langer JD, Schuman EM, (2016) "Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses." <i>Neuron</i> <b>92</b>(2):358–371; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27764671 27764671]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.09.058 10.1016/j.neuron.2016.09.058]; GPMDB: [http://gpmdb.org/data/keyword/27764671 80]. | #Schanzenbächer CT, Sambandan S, Langer JD, Schuman EM, (2016) "Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses." <i>Neuron</i> <b>92</b>(2):358–371; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27764671 27764671]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.09.058 10.1016/j.neuron.2016.09.058]; GPMDB: [http://gpmdb.org/data/keyword/27764671 80]. | ||
#Yu P, Hahne H, Wilhelm M, Kuster B, (2017) "Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics." <i>Anal Bioanal Chem</i> <b>409</b>(4):1049–1057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27766361 27766361]; doi: [https://dx.doi.org/10.1007/s00216-016-0023-x 10.1007/s00216-016-0023-x]; GPMDB: [http://gpmdb.org/data/keyword/27766361 147]. | #Yu P, Hahne H, Wilhelm M, Kuster B, (2017) "Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics." <i>Anal Bioanal Chem</i> <b>409</b>(4):1049–1057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27766361 27766361]; doi: [https://dx.doi.org/10.1007/s00216-016-0023-x 10.1007/s00216-016-0023-x]; GPMDB: [http://gpmdb.org/data/keyword/27766361 147]. | ||
+ | #Isogai T, van der Kammen R, Bleijerveld OB, Goerdayal SS, Argenzio E, Altelaar AF, Innocenti M, (2016) "Quantitative Proteomics Illuminates a Functional Interaction between mDia2 and the Proteasome." <i>J Proteome Res</i> <b>15</b>(12):4624–4637; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27769112 27769112]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00718 10.1021/acs.jproteome.6b00718]; GPMDB: [http://gpmdb.org/data/keyword/27769112 44]. | ||
#Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 25]. | #Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 25]. | ||
#Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J, (2016) "Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins." <i>Mol Cell</i> <b>64</b>(3):624–635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27773674 27773674]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.09.019 10.1016/j.molcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27773674 13]. | #Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J, (2016) "Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins." <i>Mol Cell</i> <b>64</b>(3):624–635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27773674 27773674]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.09.019 10.1016/j.molcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27773674 13]. | ||
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#Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [http://gpmdb.org/data/keyword/28914261 17]. | #Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [http://gpmdb.org/data/keyword/28914261 17]. | ||
#Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [http://gpmdb.org/data/keyword/28916541 92]. | #Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [http://gpmdb.org/data/keyword/28916541 92]. | ||
+ | #Martin-Perez M, Villén J, (2017) "Determinants and Regulation of Protein Turnover in Yeast." <i>Cell Syst</i> <b>5</b>(3):283–294.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28918244 28918244]; doi: [https://dx.doi.org/10.1016/j.cels.2017.08.008 10.1016/j.cels.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28918244 12]. | ||
#Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." <i>Cell Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28919039 28919039]; doi: [https://dx.doi.org/10.1016/j.chembiol.2017.08.006 10.1016/j.chembiol.2017.08.006]; GPMDB: [http://gpmdb.org/data/keyword/28919039 16]. | #Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." <i>Cell Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28919039 28919039]; doi: [https://dx.doi.org/10.1016/j.chembiol.2017.08.006 10.1016/j.chembiol.2017.08.006]; GPMDB: [http://gpmdb.org/data/keyword/28919039 16]. | ||
#Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, (2017) "Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection." <i>Nat Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28924191 28924191]; doi: [https://dx.doi.org/10.1038/s41564-017-0021-6 10.1038/s41564-017-0021-6]; GPMDB: [http://gpmdb.org/data/keyword/28924191 15]. | #Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, (2017) "Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection." <i>Nat Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28924191 28924191]; doi: [https://dx.doi.org/10.1038/s41564-017-0021-6 10.1038/s41564-017-0021-6]; GPMDB: [http://gpmdb.org/data/keyword/28924191 15]. | ||
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#Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | #Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | ||
#Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | #Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | ||
+ | #Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | ||
#Grenga L, Chandra G, Saalbach G, Galmozzi CV, Kramer G, Malone JG, (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." <i>Front Microbiol</i> <b>8</b>:1784; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29033902 29033902]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01784 10.3389/fmicb.2017.01784]; GPMDB: [http://gpmdb.org/data/keyword/29033902 1]. | #Grenga L, Chandra G, Saalbach G, Galmozzi CV, Kramer G, Malone JG, (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." <i>Front Microbiol</i> <b>8</b>:1784; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29033902 29033902]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01784 10.3389/fmicb.2017.01784]; GPMDB: [http://gpmdb.org/data/keyword/29033902 1]. | ||
+ | #Kugeratski FG, Batista M, Lima CVP, Neilson LJ, da Cunha ES, de Godoy LMF, Zanivan S, Krieger MA, Marchini FK, (2017) "The mitogen-activated protein kinase kinase 5 regulates the proliferation and biosynthetic processes in procyclic forms of Trypanosoma brucei." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29043805 29043805]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00415 10.1021/acs.jproteome.7b00415]; GPMDB: [http://gpmdb.org/data/keyword/29043805 15]. | ||
+ | #Raschdorf O, Bonn F, Zeytuni N, Zarivach R, Becher D, Schüler D, (2017) "A quantitative assessment of the membrane-integral sub-proteome of a bacterial magnetic organelle." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29054541 29054541]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.007 10.1016/j.jprot.2017.10.007]; GPMDB: [http://gpmdb.org/data/keyword/29054541 127]. | ||
+ | #Karg E, Smets M, Ryan J, Forné I, Qin W, Mulholland CB, Kalideris G, Imhof A, Bultmann S, Leonhardt H, (2017) "Ubiquitome analysis reveals PCNA-associated factor 15 (PAF15) as a specific ubiquitination target of UHRF1 in embryonic stem cells." <i>J Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29055779 29055779]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.10.014 10.1016/j.jmb.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29055779 32]. | ||
+ | #Hartl M, Füßl M, Boersema PJ, Jost JO, Kramer K, Bakirbas A, Sindlinger J, Plöchinger M, Leister D, Uhrig G, Moorhead GB, Cox J, Salvucci ME, Schwarzer D, Mann M, Finkemeier I, (2017) "Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in <i>Arabidopsis</i>." <i>Mol Syst Biol</i> <b>13</b>(10):949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29061669 29061669]; GPMDB: [http://gpmdb.org/data/keyword/29061669 9]. |
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.
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 Oct. 29, 2017.