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 | + | 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 6, 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 1,566: | Line 1,566: | ||
#Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, (2017) "An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28601559 28601559]; doi: [https://dx.doi.org/10.1016/j.cels.2017.05.009 10.1016/j.cels.2017.05.009]; GPMDB: [http://gpmdb.org/data/keyword/28601559 93]. | #Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, (2017) "An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28601559 28601559]; doi: [https://dx.doi.org/10.1016/j.cels.2017.05.009 10.1016/j.cels.2017.05.009]; GPMDB: [http://gpmdb.org/data/keyword/28601559 93]. | ||
#Lapek JD Jr, Lewinski MK, Wozniak JM, Guatelli J, Gonzalez DJ, (2017) "Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Vpr." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28606917 28606917]; doi: [https://dx.doi.org/10.1074/mcp.M116.066019 10.1074/mcp.M116.066019]; GPMDB: [http://gpmdb.org/data/keyword/28606917 4]. | #Lapek JD Jr, Lewinski MK, Wozniak JM, Guatelli J, Gonzalez DJ, (2017) "Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Vpr." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28606917 28606917]; doi: [https://dx.doi.org/10.1074/mcp.M116.066019 10.1074/mcp.M116.066019]; GPMDB: [http://gpmdb.org/data/keyword/28606917 4]. | ||
+ | #Brocard L, Immel F, Coulon D, Esnay N, Tuphile K, Pascal S, Claverol S, Fouillen L, Bessoule JJ, Bréhélin C, (2017) "Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions." <i>Front Plant Sci</i> <b>8</b>:894; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28611809 28611809]; doi: [https://dx.doi.org/10.3389/fpls.2017.00894 10.3389/fpls.2017.00894]; GPMDB: [http://gpmdb.org/data/keyword/28611809 3]. | ||
#Erdmann J, Junemann J, Schröder A, Just I, Gerhard R, Pich A, (2017) "Glucosyltransferase-dependent and -independent effects of TcdB on the proteome of HEp-2 cells." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28612519 28612519]; doi: [https://dx.doi.org/10.1002/pmic.201600435 10.1002/pmic.201600435]; GPMDB: [http://gpmdb.org/data/keyword/28612519 36]. | #Erdmann J, Junemann J, Schröder A, Just I, Gerhard R, Pich A, (2017) "Glucosyltransferase-dependent and -independent effects of TcdB on the proteome of HEp-2 cells." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28612519 28612519]; doi: [https://dx.doi.org/10.1002/pmic.201600435 10.1002/pmic.201600435]; GPMDB: [http://gpmdb.org/data/keyword/28612519 36]. | ||
#Murgia M, Toniolo L, Nagaraj N, Ciciliot S, Vindigni V, Schiaffino S, Reggiani C, Mann M, (2017) "Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging." <i>Cell Rep</i> <b>19</b>(11):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28614723 28614723]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.05.054 10.1016/j.celrep.2017.05.054]; GPMDB: [http://gpmdb.org/data/keyword/28614723 174]. | #Murgia M, Toniolo L, Nagaraj N, Ciciliot S, Vindigni V, Schiaffino S, Reggiani C, Mann M, (2017) "Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging." <i>Cell Rep</i> <b>19</b>(11):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28614723 28614723]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.05.054 10.1016/j.celrep.2017.05.054]; GPMDB: [http://gpmdb.org/data/keyword/28614723 174]. | ||
Line 1,576: | Line 1,577: | ||
#Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO, (2017) "Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28641008 28641008]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00144 10.1021/acs.jproteome.7b00144]; GPMDB: [http://gpmdb.org/data/keyword/28641008 39]. | #Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO, (2017) "Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28641008 28641008]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00144 10.1021/acs.jproteome.7b00144]; GPMDB: [http://gpmdb.org/data/keyword/28641008 39]. | ||
#Belmont J, Gu T, Mudd A, Salomon AR, (2017) "A PLC-γ1 Feedback Pathway Regulates Lck Substrate Phosphorylation at the T-Cell Receptor and SLP-76 Complex." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28644030 28644030]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01026 10.1021/acs.jproteome.6b01026]; GPMDB: [http://gpmdb.org/data/keyword/28644030 60]. | #Belmont J, Gu T, Mudd A, Salomon AR, (2017) "A PLC-γ1 Feedback Pathway Regulates Lck Substrate Phosphorylation at the T-Cell Receptor and SLP-76 Complex." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28644030 28644030]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01026 10.1021/acs.jproteome.6b01026]; GPMDB: [http://gpmdb.org/data/keyword/28644030 60]. | ||
+ | #Gu Y, Albuquerque CP, Braas D, Zhang W, Villa GR, Bi J, Ikegami S, Masui K, Gini B, Yang H, Gahman TC, Shiau AK, Cloughesy TF, Christofk HR, Zhou H, Guan KL, Mischel PS, (2017) "mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT." <i>Mol Cell</i> <b>67</b>(1):128–138.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648777 28648777]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.030 10.1016/j.molcel.2017.05.030]; GPMDB: [http://gpmdb.org/data/keyword/28648777 2]. | ||
#Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M, (2017) "The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1." <i>Mol Cell</i> <b>67</b>(2):294–307.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648780 28648780]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.026 10.1016/j.molcel.2017.05.026]; GPMDB: [http://gpmdb.org/data/keyword/28648780 50]. | #Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M, (2017) "The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1." <i>Mol Cell</i> <b>67</b>(2):294–307.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648780 28648780]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.026 10.1016/j.molcel.2017.05.026]; GPMDB: [http://gpmdb.org/data/keyword/28648780 50]. | ||
+ | #Morgenstern M, Stiller SB, Lübbert P, Peikert CD, Dannenmaier S, Drepper F, Weill U, Höß P, Feuerstein R, Gebert M, Bohnert M, van der Laan M, Schuldiner M, Schütze C, Oeljeklaus S, Pfanner N, Wiedemann N, Warscheid B, (2017) "Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale." <i>Cell Rep</i> <b>19</b>(13):2836–2852; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28658629 28658629]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.06.014 10.1016/j.celrep.2017.06.014]; GPMDB: [http://gpmdb.org/data/keyword/28658629 697]. | ||
+ | #Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D, (2017) "Comparison of fractionation proteomics for local SWATH library building." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28664598 28664598]; doi: [https://dx.doi.org/10.1002/pmic.201700052 10.1002/pmic.201700052]; GPMDB: [http://gpmdb.org/data/keyword/28664598 4]. | ||
#Sap KA, Bezstarosti K, Dekkers DHW, Voets O, Demmers JAA, (2017) "Quantitative Proteomics Reveals Extensive Changes in the Ubiquitinome after Perturbation of the Proteasome by Targeted dsRNA-Mediated Subunit Knockdown in Drosophila." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28665616 28665616]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00156 10.1021/acs.jproteome.7b00156]; GPMDB: [http://gpmdb.org/data/keyword/28665616 290]. | #Sap KA, Bezstarosti K, Dekkers DHW, Voets O, Demmers JAA, (2017) "Quantitative Proteomics Reveals Extensive Changes in the Ubiquitinome after Perturbation of the Proteasome by Targeted dsRNA-Mediated Subunit Knockdown in Drosophila." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28665616 28665616]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00156 10.1021/acs.jproteome.7b00156]; GPMDB: [http://gpmdb.org/data/keyword/28665616 290]. | ||
#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]. | ||
+ | #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 132]. | #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 132]. | ||
+ | #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]. | ||
+ | #Zwittink RD, van Zoeren-Grobben D, Martin R, van Lingen RA, Groot Jebbink LJ, Boeren S, Renes IB, van Elburg RM, Belzer C, Knol J, (2017) "Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28684633 28684633]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000102 10.1074/mcp.RA117.000102]; GPMDB: [http://gpmdb.org/data/keyword/28684633 65]. | ||
#Djuric U, Rodrigues DC, Batruch I, Ellis J, Shannon P, Diamandis P, (2017) "Spatiotemporal proteomic profiling of human cerebral development." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28687556 28687556]; doi: [https://dx.doi.org/10.1074/mcp.M116.066274 10.1074/mcp.M116.066274]; GPMDB: [http://gpmdb.org/data/keyword/28687556 99]. | #Djuric U, Rodrigues DC, Batruch I, Ellis J, Shannon P, Diamandis P, (2017) "Spatiotemporal proteomic profiling of human cerebral development." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28687556 28687556]; doi: [https://dx.doi.org/10.1074/mcp.M116.066274 10.1074/mcp.M116.066274]; GPMDB: [http://gpmdb.org/data/keyword/28687556 99]. | ||
#Reid SE, Kay EJ, Neilson LJ, Henze AT, Serneels J, McGhee EJ, Dhayade S, Nixon C, Mackey JB, Santi A, Swaminathan K, Athineos D, Papalazarou V, Patella F, Román-Fernández Á, ElMaghloob Y, Hernandez-Fernaud JR, Adams RH, Ismail S, Bryant DM, Salmeron-Sanchez M, Machesky LM, Carlin LM, Blyth K, Mazzone M, Zanivan S, (2017) "Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28694244 28694244]; doi: [https://dx.doi.org/10.15252/embj.201694912 10.15252/embj.201694912]; GPMDB: [http://gpmdb.org/data/keyword/28694244 19]. | #Reid SE, Kay EJ, Neilson LJ, Henze AT, Serneels J, McGhee EJ, Dhayade S, Nixon C, Mackey JB, Santi A, Swaminathan K, Athineos D, Papalazarou V, Patella F, Román-Fernández Á, ElMaghloob Y, Hernandez-Fernaud JR, Adams RH, Ismail S, Bryant DM, Salmeron-Sanchez M, Machesky LM, Carlin LM, Blyth K, Mazzone M, Zanivan S, (2017) "Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28694244 28694244]; doi: [https://dx.doi.org/10.15252/embj.201694912 10.15252/embj.201694912]; GPMDB: [http://gpmdb.org/data/keyword/28694244 19]. | ||
#Ovelleiro D, Blanco S, Hernández R, Peinado MÁ, (2017) "Comparative proteomic study of early hypoxic response in the cerebral cortex of rats submitted to two different hypoxic models." <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28697276 28697276]; doi: [https://dx.doi.org/10.1002/prca.201700058 10.1002/prca.201700058]; GPMDB: [http://gpmdb.org/data/keyword/28697276 19]. | #Ovelleiro D, Blanco S, Hernández R, Peinado MÁ, (2017) "Comparative proteomic study of early hypoxic response in the cerebral cortex of rats submitted to two different hypoxic models." <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28697276 28697276]; doi: [https://dx.doi.org/10.1002/prca.201700058 10.1002/prca.201700058]; GPMDB: [http://gpmdb.org/data/keyword/28697276 19]. | ||
+ | #Zhang X, Li L, Mayne J, Ning Z, Stintzi A, Figeys D, (2017) "Assessing the impact of protein extraction methods for human gut metaproteomics." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28705725 28705725]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.07.001 10.1016/j.jprot.2017.07.001]; GPMDB: [http://gpmdb.org/data/keyword/28705725 30]. | ||
#Kohli P, Höhne M, Jüngst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B, (2017) "The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28710093 28710093]; doi: [https://dx.doi.org/10.15252/embr.201643846 10.15252/embr.201643846]; GPMDB: [http://gpmdb.org/data/keyword/28710093 20]. | #Kohli P, Höhne M, Jüngst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B, (2017) "The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28710093 28710093]; doi: [https://dx.doi.org/10.15252/embr.201643846 10.15252/embr.201643846]; GPMDB: [http://gpmdb.org/data/keyword/28710093 20]. | ||
+ | #Hongliang L, Lei Z, Qing W, Zhaopeng S, Xiaoyan S, Juan D, Chenyang H, Yong Z, Zekun G, (2017) "Comprehensive Proteomic Analysis of PGC7-Interacting Proteins." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28712289 28712289]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00883 10.1021/acs.jproteome.6b00883]; GPMDB: [http://gpmdb.org/data/keyword/28712289 10]. | ||
+ | #Chai H, Diaz-Castro B, Shigetomi E, Monte E, Octeau JC, Yu X, Cohn W, Rajendran PS, Vondriska TM, Whitelegge JP, Coppola G, Khakh BS, (2017) "Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence." <i>Neuron</i> <b>95</b>(3):531–549.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28712653 28712653]; doi: [https://dx.doi.org/10.1016/j.neuron.2017.06.029 10.1016/j.neuron.2017.06.029]; GPMDB: [http://gpmdb.org/data/keyword/28712653 4]. | ||
#Alfieri A, Sorokina O, Adrait A, Angelini C, Russo I, Morellato A, Matteoli M, Menna E, Boeri Erba E, McLean C, Armstrong JD, Ala U, Buxbaum JD, Brusco A, Couté Y, De Rubeis S, Turco E, Defilippi P, (2017) "Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders." <i>Front Mol Neurosci</i> <b>10</b>:212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28713243 28713243]; doi: [https://dx.doi.org/10.3389/fnmol.2017.00212 10.3389/fnmol.2017.00212]; GPMDB: [http://gpmdb.org/data/keyword/28713243 12]. | #Alfieri A, Sorokina O, Adrait A, Angelini C, Russo I, Morellato A, Matteoli M, Menna E, Boeri Erba E, McLean C, Armstrong JD, Ala U, Buxbaum JD, Brusco A, Couté Y, De Rubeis S, Turco E, Defilippi P, (2017) "Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders." <i>Front Mol Neurosci</i> <b>10</b>:212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28713243 28713243]; doi: [https://dx.doi.org/10.3389/fnmol.2017.00212 10.3389/fnmol.2017.00212]; GPMDB: [http://gpmdb.org/data/keyword/28713243 12]. | ||
+ | #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 1]. | ||
+ | #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]. | ||
+ | #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]. |
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 6, 2017.