Line 25: | Line 25: | ||
==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 August | + | 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 August 13, 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]. | ||
Line 1,584: | Line 1,584: | ||
#Hulme CH, Wilson EL, Peffers MJ, Roberts S, Simpson DM, Richardson JB, Gallacher P, Wright KT, (2017) "Autologous chondrocyte implantation-derived synovial fluids display distinct responder and non-responder proteomic profiles." <i>Arthritis Res Ther</i> <b>19</b>(1):150; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28666451 28666451]; doi: [https://dx.doi.org/10.1186/s13075-017-1336-7 10.1186/s13075-017-1336-7]; GPMDB: [http://gpmdb.org/data/keyword/28666451 37]. | #Hulme CH, Wilson EL, Peffers MJ, Roberts S, Simpson DM, Richardson JB, Gallacher P, Wright KT, (2017) "Autologous chondrocyte implantation-derived synovial fluids display distinct responder and non-responder proteomic profiles." <i>Arthritis Res Ther</i> <b>19</b>(1):150; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28666451 28666451]; doi: [https://dx.doi.org/10.1186/s13075-017-1336-7 10.1186/s13075-017-1336-7]; GPMDB: [http://gpmdb.org/data/keyword/28666451 37]. | ||
#Kim JH, Nam WS, Kim SJ, Kwon OK, Seung EJ, Jo JJ, Shresha R, Lee TH, Jeon TW, Ki SH, Lee HS, Lee S, (2017) "Mechanism Investigation of Rifampicin-Induced Liver Injury Using Comparative Toxicoproteomics in Mice." <i>Int J Mol Sci</i> <b>18</b>(7):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28671602 28671602]; doi: [https://dx.doi.org/10.3390/ijms18071417 10.3390/ijms18071417]; GPMDB: [http://gpmdb.org/data/keyword/28671602 10]. | #Kim JH, Nam WS, Kim SJ, Kwon OK, Seung EJ, Jo JJ, Shresha R, Lee TH, Jeon TW, Ki SH, Lee HS, Lee S, (2017) "Mechanism Investigation of Rifampicin-Induced Liver Injury Using Comparative Toxicoproteomics in Mice." <i>Int J Mol Sci</i> <b>18</b>(7):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28671602 28671602]; doi: [https://dx.doi.org/10.3390/ijms18071417 10.3390/ijms18071417]; GPMDB: [http://gpmdb.org/data/keyword/28671602 10]. | ||
+ | #Liu F, Meng H, Fitzgerald MC, (2017) "Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using SILAC-SPROX." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28673085 28673085]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00283 10.1021/acs.jproteome.7b00283]; GPMDB: [http://gpmdb.org/data/keyword/28673085 6]. | ||
#Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F, (2017) "MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(29):7671–7676; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28673974 28673974]; doi: [https://dx.doi.org/10.1073/pnas.1620208114 10.1073/pnas.1620208114]; GPMDB: [http://gpmdb.org/data/keyword/28673974 6]. | #Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F, (2017) "MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(29):7671–7676; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28673974 28673974]; doi: [https://dx.doi.org/10.1073/pnas.1620208114 10.1073/pnas.1620208114]; GPMDB: [http://gpmdb.org/data/keyword/28673974 6]. | ||
- | #Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J, (2017) "Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome." <i>Sci Rep</i> <b>7</b>(1):4513; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28674419 28674419]; doi: [https://dx.doi.org/10.1038/s41598-017-04798-z 10.1038/s41598-017-04798-z]; GPMDB: [http://gpmdb.org/data/keyword/28674419 | + | #Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J, (2017) "Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome." <i>Sci Rep</i> <b>7</b>(1):4513; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28674419 28674419]; doi: [https://dx.doi.org/10.1038/s41598-017-04798-z 10.1038/s41598-017-04798-z]; GPMDB: [http://gpmdb.org/data/keyword/28674419 133]. |
#Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS, (2017) "Genes essential for phototrophic growth by a purple alphaproteobacterium." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28677146 28677146]; doi: [https://dx.doi.org/10.1111/1462-2920.13852 10.1111/1462-2920.13852]; GPMDB: [http://gpmdb.org/data/keyword/28677146 6]. | #Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS, (2017) "Genes essential for phototrophic growth by a purple alphaproteobacterium." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28677146 28677146]; doi: [https://dx.doi.org/10.1111/1462-2920.13852 10.1111/1462-2920.13852]; GPMDB: [http://gpmdb.org/data/keyword/28677146 6]. | ||
#Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM, (2017) "HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma." <i>Cancer Metab</i> <b>5</b>:5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28680592 28680592]; doi: [https://dx.doi.org/10.1186/s40170-017-0167-y 10.1186/s40170-017-0167-y]; GPMDB: [http://gpmdb.org/data/keyword/28680592 12]. | #Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM, (2017) "HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma." <i>Cancer Metab</i> <b>5</b>:5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28680592 28680592]; doi: [https://dx.doi.org/10.1186/s40170-017-0167-y 10.1186/s40170-017-0167-y]; GPMDB: [http://gpmdb.org/data/keyword/28680592 12]. | ||
Line 1,599: | Line 1,600: | ||
#Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S, (2017) "Outer Membrane Proteome of <i>Veillonella parvula:</i> A Diderm Firmicute of the Human Microbiome." <i>Front Microbiol</i> <b>8</b>:1215; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28713344 28713344]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01215 10.3389/fmicb.2017.01215]; GPMDB: [http://gpmdb.org/data/keyword/28713344 16]. | #Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S, (2017) "Outer Membrane Proteome of <i>Veillonella parvula:</i> A Diderm Firmicute of the Human Microbiome." <i>Front Microbiol</i> <b>8</b>:1215; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28713344 28713344]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01215 10.3389/fmicb.2017.01215]; GPMDB: [http://gpmdb.org/data/keyword/28713344 16]. | ||
#Lee HJ, Jedrychowski MP, Vinayagam A, Wu N, Shyh-Chang N, Hu Y, Min-Wen C, Moore JK, Asara JM, Lyssiotis CA, Perrimon N, Gygi SP, Cantley LC, Kirschner MW, (2017) "Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation." <i>Cell Rep</i> <b>20</b>(3):721–736; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28723573 28723573]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.06.074 10.1016/j.celrep.2017.06.074]; GPMDB: [http://gpmdb.org/data/keyword/28723573 2]. | #Lee HJ, Jedrychowski MP, Vinayagam A, Wu N, Shyh-Chang N, Hu Y, Min-Wen C, Moore JK, Asara JM, Lyssiotis CA, Perrimon N, Gygi SP, Cantley LC, Kirschner MW, (2017) "Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation." <i>Cell Rep</i> <b>20</b>(3):721–736; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28723573 28723573]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.06.074 10.1016/j.celrep.2017.06.074]; GPMDB: [http://gpmdb.org/data/keyword/28723573 2]. | ||
- | #La Barbera G, Capriotti AL, Michelini E, Piovesana S, Calabretta MM, Chiozzi RZ, Roda A, Laganà A, (2017) "Proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28727291 28727291]; doi: [https://dx.doi.org/10.1002/pmic.201700081 10.1002/pmic.201700081]; GPMDB: [http://gpmdb.org/data/keyword/28727291 | + | #La Barbera G, Capriotti AL, Michelini E, Piovesana S, Calabretta MM, Chiozzi RZ, Roda A, Laganà A, (2017) "Proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28727291 28727291]; doi: [https://dx.doi.org/10.1002/pmic.201700081 10.1002/pmic.201700081]; GPMDB: [http://gpmdb.org/data/keyword/28727291 5]. |
+ | #Hau AC, Grebbin BM, Agoston Z, Anders-Maurer M, Müller T, Groß A, Kolb J, Langer JD, Döring C, Schulte D, (2017) "MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1." <i>J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28739678 28739678]; doi: [https://dx.doi.org/10.1083/jcb.201701154 10.1083/jcb.201701154]; GPMDB: [http://gpmdb.org/data/keyword/28739678 6]. | ||
#D'Angelo G, Chaerkady R, Yu W, Hizal DB, Hess S, Zhao W, Lekstrom K, Guo X, White WI, Roskos L, Bowen MA, Yang H, (2017) "Statistical models for the analysis of isobaric tags multiplexed quantitative proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28745510 28745510]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01050 10.1021/acs.jproteome.6b01050]; GPMDB: [http://gpmdb.org/data/keyword/28745510 5]. | #D'Angelo G, Chaerkady R, Yu W, Hizal DB, Hess S, Zhao W, Lekstrom K, Guo X, White WI, Roskos L, Bowen MA, Yang H, (2017) "Statistical models for the analysis of isobaric tags multiplexed quantitative proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28745510 28745510]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01050 10.1021/acs.jproteome.6b01050]; GPMDB: [http://gpmdb.org/data/keyword/28745510 5]. | ||
#Komor MA, Pham T, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA, (2017) "Identification of differentially expressed splice variants by the proteogenomic pipeline Splicify." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28747380 28747380]; doi: [https://dx.doi.org/10.1074/mcp.TIR117.000056 10.1074/mcp.TIR117.000056]; GPMDB: [http://gpmdb.org/data/keyword/28747380 14]. | #Komor MA, Pham T, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA, (2017) "Identification of differentially expressed splice variants by the proteogenomic pipeline Splicify." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28747380 28747380]; doi: [https://dx.doi.org/10.1074/mcp.TIR117.000056 10.1074/mcp.TIR117.000056]; GPMDB: [http://gpmdb.org/data/keyword/28747380 14]. | ||
#Gómez-Baena G, Bennett RJ, Martínez-Rodríguez C, Wnęk M, Laing G, Hickey G, McLean L, Beynon RJ, Carrol ED, (2017) "Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis." <i>Sci Rep</i> <b>7</b>(1):7042; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28765563 28765563]; doi: [https://dx.doi.org/10.1038/s41598-017-07127-6 10.1038/s41598-017-07127-6]; GPMDB: [http://gpmdb.org/data/keyword/28765563 28]. | #Gómez-Baena G, Bennett RJ, Martínez-Rodríguez C, Wnęk M, Laing G, Hickey G, McLean L, Beynon RJ, Carrol ED, (2017) "Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis." <i>Sci Rep</i> <b>7</b>(1):7042; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28765563 28765563]; doi: [https://dx.doi.org/10.1038/s41598-017-07127-6 10.1038/s41598-017-07127-6]; GPMDB: [http://gpmdb.org/data/keyword/28765563 28]. | ||
+ | #Woo J, Han D, Wang JI, Park J, Kim H, Kim Y, (2017) "Quantitative proteomics reveal temporal proteomic changes in signaling pathways during BV2 mouse microglial cell activation." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28777000 28777000]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00445 10.1021/acs.jproteome.7b00445]; GPMDB: [http://gpmdb.org/data/keyword/28777000 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.
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 August 13, 2017.