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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 December | + | 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 December 18, 2016. |
#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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#Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M, (2015) "DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links." <i>Science</i> <b>348</b>(6234):1253671; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25931565 25931565]; doi: [https://dx.doi.org/10.1126/science.1253671 10.1126/science.1253671]; GPMDB: [http://gpmdb.org/data/keyword/25931565 21]. | #Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M, (2015) "DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links." <i>Science</i> <b>348</b>(6234):1253671; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25931565 25931565]; doi: [https://dx.doi.org/10.1126/science.1253671 10.1126/science.1253671]; GPMDB: [http://gpmdb.org/data/keyword/25931565 21]. | ||
#Penzo M, Rocchi L, Brugiere S, Carnicelli D, Onofrillo C, Couté Y, Brigotti M, Montanaro L, (2015) "Human ribosomes from cells with reduced dyskerin levels are intrinsically altered in translation." <i>FASEB J</i> <b>29</b>(8):3472–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25934701 25934701]; doi: [https://dx.doi.org/10.1096/fj.15-270991 10.1096/fj.15-270991]; GPMDB: [http://gpmdb.org/data/keyword/25934701 20]. | #Penzo M, Rocchi L, Brugiere S, Carnicelli D, Onofrillo C, Couté Y, Brigotti M, Montanaro L, (2015) "Human ribosomes from cells with reduced dyskerin levels are intrinsically altered in translation." <i>FASEB J</i> <b>29</b>(8):3472–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25934701 25934701]; doi: [https://dx.doi.org/10.1096/fj.15-270991 10.1096/fj.15-270991]; GPMDB: [http://gpmdb.org/data/keyword/25934701 20]. | ||
+ | #Böhm G, Prefot P, Jung S, Selzer S, Mitra V, Britton D, Kuhn K, Pike I, Thompson AH, (2015) "Low-pH Solid-Phase Amino Labeling of Complex Peptide Digests with TMTs Improves Peptide Identification Rates for Multiplexed Global Phosphopeptide Analysis." <i>J Proteome Res</i> <b>14</b>(6):2500–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25939058 25939058]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00072 10.1021/acs.jproteome.5b00072]; GPMDB: [http://gpmdb.org/data/keyword/25939058 18]. | ||
#Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E, (2015) "A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery." <i>J Proteome Res</i> <b>14</b>(7):2807–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25944384 25944384]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00315 10.1021/acs.jproteome.5b00315]; GPMDB: [http://gpmdb.org/data/keyword/25944384 238]. | #Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E, (2015) "A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery." <i>J Proteome Res</i> <b>14</b>(7):2807–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25944384 25944384]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00315 10.1021/acs.jproteome.5b00315]; GPMDB: [http://gpmdb.org/data/keyword/25944384 238]. | ||
#Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA, (2015) "Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow." <i>Mol Cell Proteomics</i> <b>14</b>(9):2429–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25953088 25953088]; doi: [https://dx.doi.org/10.1074/mcp.O114.047555 10.1074/mcp.O114.047555]; GPMDB: [http://gpmdb.org/data/keyword/25953088 30]. | #Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA, (2015) "Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow." <i>Mol Cell Proteomics</i> <b>14</b>(9):2429–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25953088 25953088]; doi: [https://dx.doi.org/10.1074/mcp.O114.047555 10.1074/mcp.O114.047555]; GPMDB: [http://gpmdb.org/data/keyword/25953088 30]. | ||
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#Horton ER, Byron A, Askari JA, Ng DH, Millon-Frémillon A, Robertson J, Koper EJ, Paul NR, Warwood S, Knight D, Humphries JD, Humphries MJ, (2015) "Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly." <i>Nat Cell Biol</i> <b>17</b>(12):1577–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26479319 26479319]; doi: [https://dx.doi.org/10.1038/ncb3257 10.1038/ncb3257]; GPMDB: [http://gpmdb.org/data/keyword/26479319 100]. | #Horton ER, Byron A, Askari JA, Ng DH, Millon-Frémillon A, Robertson J, Koper EJ, Paul NR, Warwood S, Knight D, Humphries JD, Humphries MJ, (2015) "Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly." <i>Nat Cell Biol</i> <b>17</b>(12):1577–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26479319 26479319]; doi: [https://dx.doi.org/10.1038/ncb3257 10.1038/ncb3257]; GPMDB: [http://gpmdb.org/data/keyword/26479319 100]. | ||
#Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M, (2015) "A human interactome in three quantitative dimensions organized by stoichiometries and abundances." <i>Cell</i> <b>163</b>(3):712–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26496610 26496610]; doi: [https://dx.doi.org/10.1016/j.cell.2015.09.053 10.1016/j.cell.2015.09.053]; GPMDB: [http://gpmdb.org/data/keyword/26496610 4296]. | #Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M, (2015) "A human interactome in three quantitative dimensions organized by stoichiometries and abundances." <i>Cell</i> <b>163</b>(3):712–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26496610 26496610]; doi: [https://dx.doi.org/10.1016/j.cell.2015.09.053 10.1016/j.cell.2015.09.053]; GPMDB: [http://gpmdb.org/data/keyword/26496610 4296]. | ||
+ | #Isasa M, Rose CM, Elsasser S, Navarrete-Perea J, Paulo JA, Finley DJ, Gygi SP, (2015) "Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains." <i>J Proteome Res</i> <b>14</b>(12):5306–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26503604 26503604]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00802 10.1021/acs.jproteome.5b00802]; GPMDB: [http://gpmdb.org/data/keyword/26503604 4]. | ||
#Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC, Juan HF, (2015) "Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin." <i>Mol Cell Proteomics</i> <b>14</b>(12):3284–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26503892 26503892]; doi: [https://dx.doi.org/10.1074/mcp.M115.051383 10.1074/mcp.M115.051383]; GPMDB: [http://gpmdb.org/data/keyword/26503892 48]. | #Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC, Juan HF, (2015) "Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin." <i>Mol Cell Proteomics</i> <b>14</b>(12):3284–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26503892 26503892]; doi: [https://dx.doi.org/10.1074/mcp.M115.051383 10.1074/mcp.M115.051383]; GPMDB: [http://gpmdb.org/data/keyword/26503892 48]. | ||
#O'Connor HF, Lyon N, Leung JW, Agarwal P, Swaim CD, Miller KM, Huibregtse JM, (2015) "Ubiquitin-Activated Interaction Traps (UBAITs) identify E3 ligase binding partners." <i>EMBO Rep</i> <b>16</b>(12):1699–712; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26508657 26508657]; doi: [https://dx.doi.org/10.15252/embr.201540620 10.15252/embr.201540620]; GPMDB: [http://gpmdb.org/data/keyword/26508657 74]. | #O'Connor HF, Lyon N, Leung JW, Agarwal P, Swaim CD, Miller KM, Huibregtse JM, (2015) "Ubiquitin-Activated Interaction Traps (UBAITs) identify E3 ligase binding partners." <i>EMBO Rep</i> <b>16</b>(12):1699–712; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26508657 26508657]; doi: [https://dx.doi.org/10.15252/embr.201540620 10.15252/embr.201540620]; GPMDB: [http://gpmdb.org/data/keyword/26508657 74]. | ||
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#Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2016) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i> <b>16</b>(4):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | #Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2016) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i> <b>16</b>(4):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | ||
#Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | #Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | ||
+ | #Vartanian S, Ma TP, Lee J, Haverty PM, Kirkpatrick DS, Yu K, Stokoe D, (2016) "Application of Mass Spectrometry Profiling to Establish Brusatol as an Inhibitor of Global Protein Synthesis." <i>Mol Cell Proteomics</i> <b>15</b>(4):1220–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711467 26711467]; doi: [https://dx.doi.org/10.1074/mcp.M115.055509 10.1074/mcp.M115.055509]; GPMDB: [http://gpmdb.org/data/keyword/26711467 4]. | ||
# () "" <i></i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/ ]; GPMDB: [http://gpmdb.org/data/keyword/26714523 16]. | # () "" <i></i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/ ]; GPMDB: [http://gpmdb.org/data/keyword/26714523 16]. | ||
#Bode D, Yu L, Tate P, Pardo M, Choudhary J, (2016) "Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells." <i>Mol Cell Proteomics</i> <b>15</b>(3):878–91; 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 J, (2016) "Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells." <i>Mol Cell Proteomics</i> <b>15</b>(3):878–91; 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]. | ||
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#Mattei B, Spinelli F, Pontiggia D, De Lorenzo G, (2016) "Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27532006 27532006]; doi: [https://dx.doi.org/10.3389/fpls.2016.01107 10.3389/fpls.2016.01107]; GPMDB: [http://gpmdb.org/data/keyword/27532006 12]. | #Mattei B, Spinelli F, Pontiggia D, De Lorenzo G, (2016) "Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27532006 27532006]; doi: [https://dx.doi.org/10.3389/fpls.2016.01107 10.3389/fpls.2016.01107]; GPMDB: [http://gpmdb.org/data/keyword/27532006 12]. | ||
#Solari FA, Mattheij NJ, Burkhart JM, Swieringa F, Collins PW, Cosemans JM, Sickmann A, Heemskerk JW, Zahedi RP, (2016) "Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome." <i>Mol Cell Proteomics</i> <b>15</b>(10):3154–3169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535140 27535140]; doi: [https://dx.doi.org/10.1074/mcp.M116.060368 10.1074/mcp.M116.060368]; GPMDB: [http://gpmdb.org/data/keyword/27535140 23]. | #Solari FA, Mattheij NJ, Burkhart JM, Swieringa F, Collins PW, Cosemans JM, Sickmann A, Heemskerk JW, Zahedi RP, (2016) "Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome." <i>Mol Cell Proteomics</i> <b>15</b>(10):3154–3169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535140 27535140]; doi: [https://dx.doi.org/10.1074/mcp.M116.060368 10.1074/mcp.M116.060368]; GPMDB: [http://gpmdb.org/data/keyword/27535140 23]. | ||
+ | #Wei W, Luo W, Wu F, Peng X, Zhang Y, Zhang M, Zhao Y, Su N, Qi Y, Chen L, Zhang Y, Wen B, He F, Xu P, (2016) "Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer." <i>J Proteome Res</i> <b>15</b>(11):3988–3997; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535590 27535590]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00390 10.1021/acs.jproteome.6b00390]; GPMDB: [http://gpmdb.org/data/keyword/27535590 150]. | ||
#Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | #Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | ||
#Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | #Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | ||
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#Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS, (2016) "In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis; presenting a comprehensive picture of pathways and processes affected by multiple sclerosis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27728768 27728768]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00659 10.1021/acs.jproteome.6b00659]; GPMDB: [http://gpmdb.org/data/keyword/27728768 26]. | #Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS, (2016) "In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis; presenting a comprehensive picture of pathways and processes affected by multiple sclerosis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27728768 27728768]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00659 10.1021/acs.jproteome.6b00659]; GPMDB: [http://gpmdb.org/data/keyword/27728768 26]. | ||
#Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium., Flicek P, Parkinson H, Clarke L, (2016) "The human-induced pluripotent stem cell initiative-data resources for cellular genetics." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27733501 27733501]; doi: [https://dx.doi.org/10.1093/nar/gkw928 10.1093/nar/gkw928]; GPMDB: [http://gpmdb.org/data/keyword/27733501 20]. | #Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium., Flicek P, Parkinson H, Clarke L, (2016) "The human-induced pluripotent stem cell initiative-data resources for cellular genetics." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27733501 27733501]; doi: [https://dx.doi.org/10.1093/nar/gkw928 10.1093/nar/gkw928]; GPMDB: [http://gpmdb.org/data/keyword/27733501 20]. | ||
+ | #Kuzmanov U, Guo H, Buchsbaum D, Cosme J, Abbasi C, Isserlin R, Sharma P, Gramolini AO, Emili A, (2016) "Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(44):12592–12597; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27742792 27742792]; doi: [https://dx.doi.org/10.1073/pnas.1606444113 10.1073/pnas.1606444113]; GPMDB: [http://gpmdb.org/data/keyword/27742792 86]. | ||
+ | #Sebé-Pedrós A, Peña MI, Capella-Gutiérrez S, Antó M, Gabaldón T, Ruiz-Trillo I, Sabidó E, (2016) "High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation." <i>Dev Cell</i> <b>39</b>(2):186–197; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27746046 27746046]; doi: [https://dx.doi.org/10.1016/j.devcel.2016.09.019 10.1016/j.devcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27746046 30]. | ||
+ | #Liljedahl L, Pedersen MH, Norlin J, McGuire JN, James P, (2016) "N-glycosylation proteome enrichment analysis in kidney reveals differences between diabetic mouse models." <i>Clin Proteomics</i> <b>13</b>:22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757071 27757071]; doi: [https://dx.doi.org/10.1186/s12014-016-9123-z 10.1186/s12014-016-9123-z]; GPMDB: [http://gpmdb.org/data/keyword/27757071 48]. | ||
#Zammit CM, Weiland F, Brugger J, Wade B, Winderbaum LJ, Nies DH, Southam G, Hoffmann P, Reith F, (2016) "Proteomic responses to gold(iii)-toxicity in the bacterium Cupriavidus metallidurans CH34." <i>Metallomics</i> <b>8</b>(11):1204–1216; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757465 27757465]; doi: [https://dx.doi.org/10.1039/c6mt00142d 10.1039/c6mt00142d]; GPMDB: [http://gpmdb.org/data/keyword/27757465 56]. | #Zammit CM, Weiland F, Brugger J, Wade B, Winderbaum LJ, Nies DH, Southam G, Hoffmann P, Reith F, (2016) "Proteomic responses to gold(iii)-toxicity in the bacterium Cupriavidus metallidurans CH34." <i>Metallomics</i> <b>8</b>(11):1204–1216; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757465 27757465]; doi: [https://dx.doi.org/10.1039/c6mt00142d 10.1039/c6mt00142d]; GPMDB: [http://gpmdb.org/data/keyword/27757465 56]. | ||
+ | #Sialana FJ, Gulyassy P, Májek P, Sjöstedt E, Kis V, Müller AC, Rudashevskaya EL, Mulder J, Bennett KL, Lubec G, (2016) "Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels." <i>Proteomics</i> <b>16</b>(22):2911–2920; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27759936 27759936]; doi: [https://dx.doi.org/10.1002/pmic.201600234 10.1002/pmic.201600234]; GPMDB: [http://gpmdb.org/data/keyword/27759936 68]. | ||
#Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | #Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | ||
+ | #Assoni AF, Castello G, Valadares M, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different donors Mesenchymal Stromal Cells secretomes reveal heterogeneous profile of relevance for therapeutic use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. | ||
#Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | #Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | ||
#Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | #Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | ||
- | #Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | + | #Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. |
+ | #Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i> <b>129</b>(24):4466–4479; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | ||
#Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, Cowen LE, (2016) "Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity." <i>G3 (Bethesda)</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807047 27807047]; doi: [https://dx.doi.org/10.1534/g3.116.035675 10.1534/g3.116.035675]; GPMDB: [http://gpmdb.org/data/keyword/27807047 6]. | #Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, Cowen LE, (2016) "Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity." <i>G3 (Bethesda)</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807047 27807047]; doi: [https://dx.doi.org/10.1534/g3.116.035675 10.1534/g3.116.035675]; GPMDB: [http://gpmdb.org/data/keyword/27807047 6]. | ||
- | #Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR, (2016) "Multiparameter functional diversity of human C2H2 zinc finger proteins." <i>Genome Res</i> <b>26</b>(12):1742–1752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27852650 27852650]; doi: [https://dx.doi.org/10.1101/gr.209643.116 10.1101/gr.209643.116]; GPMDB: [http://gpmdb.org/data/keyword/27852650 | + | #Chen Y, Xie Y, Xu L, Zhan S, Xiao Y, Gao Y, Wu B, Ge W, (2016) "Protein content and functional characteristics of serum-purified exosomes from patients with colorectal cancer revealed by quantitative proteomics." <i>Int J Cancer</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27813080 27813080]; doi: [https://dx.doi.org/10.1002/ijc.30496 10.1002/ijc.30496]; GPMDB: [http://gpmdb.org/data/keyword/27813080 1]. |
+ | #Kogel U, Titz B, Schlage WK, Nury C, Martin F, Oviedo A, Lebrun S, Elamin A, Guedj E, Trivedi K, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J, (2016) "Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke." <i>Regul Toxicol Pharmacol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818347 27818347]; doi: [https://dx.doi.org/10.1016/j.yrtph.2016.11.001 10.1016/j.yrtph.2016.11.001]; GPMDB: [http://gpmdb.org/data/keyword/27818347 26]. | ||
+ | #Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR, (2016) "Multiparameter functional diversity of human C2H2 zinc finger proteins." <i>Genome Res</i> <b>26</b>(12):1742–1752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27852650 27852650]; doi: [https://dx.doi.org/10.1101/gr.209643.116 10.1101/gr.209643.116]; GPMDB: [http://gpmdb.org/data/keyword/27852650 224]. | ||
#Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." <i>Nat Commun</i> <b>7</b>:13404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27869121 27869121]; doi: [https://dx.doi.org/10.1038/ncomms13404 10.1038/ncomms13404]; GPMDB: [http://gpmdb.org/data/keyword/27869121 138]. | #Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." <i>Nat Commun</i> <b>7</b>:13404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27869121 27869121]; doi: [https://dx.doi.org/10.1038/ncomms13404 10.1038/ncomms13404]; GPMDB: [http://gpmdb.org/data/keyword/27869121 138]. | ||
#St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. | #St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. | ||
#Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | #Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | ||
+ | #Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." <i>Neuron</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27916455 27916455]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.10.064 10.1016/j.neuron.2016.10.064]; GPMDB: [http://gpmdb.org/data/keyword/27916455 368]. |
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 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 December 18, 2016.