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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 January | + | 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 January 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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#Farrelly LA, Dicker P, Wynne K, English J, Cagney G, Föcking M, Cotter DR, (2014) "Adolescent Risperidone treatment alters protein expression associated with protein trafficking and cellular metabolism in the adult rat prefrontal cortex." <i>Proteomics</i> <b>14</b>(12):1574–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24733778 24733778]; doi: [https://dx.doi.org/10.1002/pmic.201300466 10.1002/pmic.201300466]; GPMDB: [http://gpmdb.org/data/keyword/24733778 30]. | #Farrelly LA, Dicker P, Wynne K, English J, Cagney G, Föcking M, Cotter DR, (2014) "Adolescent Risperidone treatment alters protein expression associated with protein trafficking and cellular metabolism in the adult rat prefrontal cortex." <i>Proteomics</i> <b>14</b>(12):1574–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24733778 24733778]; doi: [https://dx.doi.org/10.1002/pmic.201300466 10.1002/pmic.201300466]; GPMDB: [http://gpmdb.org/data/keyword/24733778 30]. | ||
#Tran DT, Adhikari J, Fitzgerald MC, (2014) "StableIsotope Labeling with Amino Acids in Cell Culture (SILAC)-based strategy for proteome-wide thermodynamic analysis of protein-ligand binding interactions." <i>Mol Cell Proteomics</i> <b>13</b>(7):1800–13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24741112 24741112]; doi: [https://dx.doi.org/10.1074/mcp.M113.034702 10.1074/mcp.M113.034702]; GPMDB: [http://gpmdb.org/data/keyword/24741112 27]. | #Tran DT, Adhikari J, Fitzgerald MC, (2014) "StableIsotope Labeling with Amino Acids in Cell Culture (SILAC)-based strategy for proteome-wide thermodynamic analysis of protein-ligand binding interactions." <i>Mol Cell Proteomics</i> <b>13</b>(7):1800–13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24741112 24741112]; doi: [https://dx.doi.org/10.1074/mcp.M113.034702 10.1074/mcp.M113.034702]; GPMDB: [http://gpmdb.org/data/keyword/24741112 27]. | ||
+ | #Kuhlmann K, Tschapek A, Wiese H, Eisenacher M, Meyer HE, Hatt HH, Oeljeklaus S, Warscheid B, (2014) "The membrane proteome of sensory cilia to the depth of olfactory receptors." <i>Mol Cell Proteomics</i> <b>13</b>(7):1828–43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24748648 24748648]; doi: [https://dx.doi.org/10.1074/mcp.M113.035378 10.1074/mcp.M113.035378]; GPMDB: [http://gpmdb.org/data/keyword/24748648 91]. | ||
#Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, Bönisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A, (2014) "The histone variant H2A.Bbd is enriched at sites of DNA synthesis." <i>Nucleic Acids Res</i> <b>42</b>(10):6405–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24753410 24753410]; doi: [https://dx.doi.org/10.1093/nar/gku303 10.1093/nar/gku303]; GPMDB: [http://gpmdb.org/data/keyword/24753410 96]. | #Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, Bönisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A, (2014) "The histone variant H2A.Bbd is enriched at sites of DNA synthesis." <i>Nucleic Acids Res</i> <b>42</b>(10):6405–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24753410 24753410]; doi: [https://dx.doi.org/10.1093/nar/gku303 10.1093/nar/gku303]; GPMDB: [http://gpmdb.org/data/keyword/24753410 96]. | ||
#Han D, Jin J, Woo J, Min H, Kim Y, (2014) "Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation." <i>Proteomics</i> <b>14</b>(13-14):1604–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24753479 24753479]; doi: [https://dx.doi.org/10.1002/pmic.201300495 10.1002/pmic.201300495]; GPMDB: [http://gpmdb.org/data/keyword/24753479 107]. | #Han D, Jin J, Woo J, Min H, Kim Y, (2014) "Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation." <i>Proteomics</i> <b>14</b>(13-14):1604–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24753479 24753479]; doi: [https://dx.doi.org/10.1002/pmic.201300495 10.1002/pmic.201300495]; GPMDB: [http://gpmdb.org/data/keyword/24753479 107]. | ||
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#Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | #Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | ||
#Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | #Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | ||
- | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 | + | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 842]. |
#Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | #Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | ||
#Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | #Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | ||
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#Zhao Y, Valbuena G, Walker DH, Gazi M, Hidalgo M, DeSousa R, Oteo JA, Goez Y, Brasier AR, (2016) "Endothelial Cell Proteomic Response to Rickettsia conorii Infection Reveals Activation of the Janus Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT)-Inferferon Stimulated Gene (ISG)15 Pathway and Reprogramming Plasma Membrane Integrin/Cadherin Signaling." <i>Mol Cell Proteomics</i> <b>15</b>(1):289–304; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560068 26560068]; doi: [https://dx.doi.org/10.1074/mcp.M115.054361 10.1074/mcp.M115.054361]; GPMDB: [http://gpmdb.org/data/keyword/26560068 7]. | #Zhao Y, Valbuena G, Walker DH, Gazi M, Hidalgo M, DeSousa R, Oteo JA, Goez Y, Brasier AR, (2016) "Endothelial Cell Proteomic Response to Rickettsia conorii Infection Reveals Activation of the Janus Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT)-Inferferon Stimulated Gene (ISG)15 Pathway and Reprogramming Plasma Membrane Integrin/Cadherin Signaling." <i>Mol Cell Proteomics</i> <b>15</b>(1):289–304; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560068 26560068]; doi: [https://dx.doi.org/10.1074/mcp.M115.054361 10.1074/mcp.M115.054361]; GPMDB: [http://gpmdb.org/data/keyword/26560068 7]. | ||
#Tutakhel OA, Jeleń S, Valdez-Flores M, Dimke H, Piersma SR, Jimenez CR, Deinum J, Lenders JW, Hoenderop JG, Bindels RJ, (2016) "Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling." <i>Am J Physiol Renal Physiol</i> <b>310</b>(3):F204–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26561651 26561651]; doi: [https://dx.doi.org/10.1152/ajprenal.00429.2015 10.1152/ajprenal.00429.2015]; GPMDB: [http://gpmdb.org/data/keyword/26561651 2]. | #Tutakhel OA, Jeleń S, Valdez-Flores M, Dimke H, Piersma SR, Jimenez CR, Deinum J, Lenders JW, Hoenderop JG, Bindels RJ, (2016) "Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling." <i>Am J Physiol Renal Physiol</i> <b>310</b>(3):F204–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26561651 26561651]; doi: [https://dx.doi.org/10.1152/ajprenal.00429.2015 10.1152/ajprenal.00429.2015]; GPMDB: [http://gpmdb.org/data/keyword/26561651 2]. | ||
+ | #Slavov N, Semrau S, Airoldi E, Budnik B, van Oudenaarden A, (2015) "Differential Stoichiometry among Core Ribosomal Proteins." <i>Cell Rep</i> <b>13</b>(5):865–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26565899 26565899]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.09.056 10.1016/j.celrep.2015.09.056]; GPMDB: [http://gpmdb.org/data/keyword/26565899 16]. | ||
#Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | #Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | ||
#Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | #Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | ||
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#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> <b>92</b>(6):1220–1237; 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 377]. | #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> <b>92</b>(6):1220–1237; 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 377]. | ||
#Tiberti N, Latham SL, Bush S, Cohen A, Opoka RO, John CC, Juillard A, Grau GE, Combes V, (2016) "Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content." <i>Sci Rep</i> <b>6</b>:37871; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27917875 27917875]; doi: [https://dx.doi.org/10.1038/srep37871 10.1038/srep37871]; GPMDB: [http://gpmdb.org/data/keyword/27917875 4]. | #Tiberti N, Latham SL, Bush S, Cohen A, Opoka RO, John CC, Juillard A, Grau GE, Combes V, (2016) "Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content." <i>Sci Rep</i> <b>6</b>:37871; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27917875 27917875]; doi: [https://dx.doi.org/10.1038/srep37871 10.1038/srep37871]; GPMDB: [http://gpmdb.org/data/keyword/27917875 4]. | ||
+ | #Tedeschi G, Albani E, Borroni EM, Parini V, Brucculeri AM, Maffioli E, Negri A, Nonnis S, Maccarrone M, Levi-Setti PE, (2016) "Proteomic profile of maternal-aged blastocoel fluid suggests a novel role for ubiquitin system in blastocyst quality." <i>J Assist Reprod Genet</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27924460 27924460]; doi: [https://dx.doi.org/10.1007/s10815-016-0842-x 10.1007/s10815-016-0842-x]; GPMDB: [http://gpmdb.org/data/keyword/27924460 10]. | ||
#Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM, (2016) "Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition." <i>J Proteome Res</i> <b>15</b>(12):4476–4489; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27934295 27934295]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00613 10.1021/acs.jproteome.6b00613]; GPMDB: [http://gpmdb.org/data/keyword/27934295 18]. | #Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM, (2016) "Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition." <i>J Proteome Res</i> <b>15</b>(12):4476–4489; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27934295 27934295]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00613 10.1021/acs.jproteome.6b00613]; GPMDB: [http://gpmdb.org/data/keyword/27934295 18]. | ||
#Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27959563 27959563]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00834 10.1021/acs.jproteome.6b00834]; GPMDB: [http://gpmdb.org/data/keyword/27959563 6]. | #Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27959563 27959563]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00834 10.1021/acs.jproteome.6b00834]; GPMDB: [http://gpmdb.org/data/keyword/27959563 6]. | ||
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#Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC, (2016) "VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28007913 28007913]; doi: [https://dx.doi.org/10.1074/mcp.M116.064428 10.1074/mcp.M116.064428]; GPMDB: [http://gpmdb.org/data/keyword/28007913 89]. | #Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC, (2016) "VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28007913 28007913]; doi: [https://dx.doi.org/10.1074/mcp.M116.064428 10.1074/mcp.M116.064428]; GPMDB: [http://gpmdb.org/data/keyword/28007913 89]. | ||
#Geyer PE, Wewer Albrechtsen NJ, Tyanova S, Grassl N, Iepsen EW, Lundgren J, Madsbad S, Holst JJ, Torekov SS, Mann M, (2016) "Proteomics reveals the effects of sustained weight loss on the human plasma proteome." <i>Mol Syst Biol</i> <b>12</b>(12):901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28007936 28007936]; GPMDB: [http://gpmdb.org/data/keyword/28007936 1145]. | #Geyer PE, Wewer Albrechtsen NJ, Tyanova S, Grassl N, Iepsen EW, Lundgren J, Madsbad S, Holst JJ, Torekov SS, Mann M, (2016) "Proteomics reveals the effects of sustained weight loss on the human plasma proteome." <i>Mol Syst Biol</i> <b>12</b>(12):901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28007936 28007936]; GPMDB: [http://gpmdb.org/data/keyword/28007936 1145]. | ||
- | #Reimann L, Wiese H, Leber Y, Schwäble AN, Fricke AL, Rohland A, Knapp B, Peikert CD, Drepper F, van der Ven PF, Radziwill G, Fürst DO, Warscheid B, (2016) "Myofibrillar Z-discs are a protein phosphorylation hot spot with PKC α modulating protein dynamics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28028127 28028127]; doi: [https://dx.doi.org/10.1074/mcp.M116.065425 10.1074/mcp.M116.065425]; GPMDB: [http://gpmdb.org/data/keyword/28028127 | + | #Reimann L, Wiese H, Leber Y, Schwäble AN, Fricke AL, Rohland A, Knapp B, Peikert CD, Drepper F, van der Ven PF, Radziwill G, Fürst DO, Warscheid B, (2016) "Myofibrillar Z-discs are a protein phosphorylation hot spot with PKC α modulating protein dynamics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28028127 28028127]; doi: [https://dx.doi.org/10.1074/mcp.M116.065425 10.1074/mcp.M116.065425]; GPMDB: [http://gpmdb.org/data/keyword/28028127 278]. |
+ | #Rougemont B, Bontemps Gallo S, Ayciriex S, Carriere R, Hondermarck H, Lacroix JM, Le Blanc JC, Lemoine J, (2016) "Scout-MRM: multiplexed targeted mass spectrometry-based assay without retention time scheduling exemplified by Dickeya dadantii proteomic analysis during plant infection." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28029036 28029036]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b03201 10.1021/acs.analchem.6b03201]; GPMDB: [http://gpmdb.org/data/keyword/28029036 8]. | ||
#Hickox AE, Wong AC, Pak K, Strojny C, Ramirez M, Yates JR Rd, Ryan AF, Savas JN, (2016) "Global Analysis of Protein Expression of Inner Ear Hair Cells." <i>J Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28039372 28039372]; doi: [https://dx.doi.org/10.1523/JNEUROSCI.2267-16.2016 10.1523/JNEUROSCI.2267-16.2016]; GPMDB: [http://gpmdb.org/data/keyword/28039372 71]. | #Hickox AE, Wong AC, Pak K, Strojny C, Ramirez M, Yates JR Rd, Ryan AF, Savas JN, (2016) "Global Analysis of Protein Expression of Inner Ear Hair Cells." <i>J Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28039372 28039372]; doi: [https://dx.doi.org/10.1523/JNEUROSCI.2267-16.2016 10.1523/JNEUROSCI.2267-16.2016]; GPMDB: [http://gpmdb.org/data/keyword/28039372 71]. | ||
+ | #Hansson KT, Skillbäck T, Pernevik E, Kern S, Portelius E, Höglund K, Brinkmalm G, Holmén-Larsson J, Blennow K, Zetterberg H, Gobom J, (2017) "Expanding the cerebrospinal fluid endopeptidome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28044435 28044435]; doi: [https://dx.doi.org/10.1002/pmic.201600384 10.1002/pmic.201600384]; GPMDB: [http://gpmdb.org/data/keyword/28044435 13]. | ||
#Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR, (2017) "Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics." <i>Cell Rep</i> <b>18</b>(1):237–247; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052253 28052253]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.013 10.1016/j.celrep.2016.12.013]; GPMDB: [http://gpmdb.org/data/keyword/28052253 128]. | #Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR, (2017) "Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics." <i>Cell Rep</i> <b>18</b>(1):237–247; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052253 28052253]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.013 10.1016/j.celrep.2016.12.013]; GPMDB: [http://gpmdb.org/data/keyword/28052253 128]. | ||
- | #Cristobal A, van den Toorn HW, van de Wetering M, Clevers H, Heck AJ, Mohammed S, (2017) "Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer." <i>Cell Rep</i> <b>18</b>(1):263–274; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052255 28052255]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.016 10.1016/j.celrep.2016.12.016]; GPMDB: [http://gpmdb.org/data/keyword/28052255 | + | #Cristobal A, van den Toorn HW, van de Wetering M, Clevers H, Heck AJ, Mohammed S, (2017) "Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer." <i>Cell Rep</i> <b>18</b>(1):263–274; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052255 28052255]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.016 10.1016/j.celrep.2016.12.016]; GPMDB: [http://gpmdb.org/data/keyword/28052255 175]. |
#Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | #Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | ||
#Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28058811 28058811]; doi: [https://dx.doi.org/10.1002/pmic.201600213 10.1002/pmic.201600213]; GPMDB: [http://gpmdb.org/data/keyword/28058811 70]. | #Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28058811 28058811]; doi: [https://dx.doi.org/10.1002/pmic.201600213 10.1002/pmic.201600213]; GPMDB: [http://gpmdb.org/data/keyword/28058811 70]. | ||
+ | #Clotet S, Soler MJ, Riera M, Pascual J, Fang F, Zhou J, Batruch I, Vasiliou SK, Dimitromanolakis A, Barrios C, Diamandis E, Scholey J, Konvalinka A, (2017) "SILAC-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062795 28062795]; doi: [https://dx.doi.org/10.1074/mcp.M116.061903 10.1074/mcp.M116.061903]; GPMDB: [http://gpmdb.org/data/keyword/28062795 4]. | ||
#Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062796 28062796]; doi: [https://dx.doi.org/10.1074/mcp.M116.063511 10.1074/mcp.M116.063511]; GPMDB: [http://gpmdb.org/data/keyword/28062796 166]. | #Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062796 28062796]; doi: [https://dx.doi.org/10.1074/mcp.M116.063511 10.1074/mcp.M116.063511]; GPMDB: [http://gpmdb.org/data/keyword/28062796 166]. | ||
- | #Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 | + | #Pietzner M, Engelmann B, Kacprowski T, Golchert J, Dirk AL, Hammer E, Iwen KA, Nauck M, Wallaschofski H, Führer D, Münte TF, Friedrich N, Völker U, Homuth G, Brabant G, (2017) "Plasma proteome and metabolome characterization of an experimental human thyrotoxicosis model." <i>BMC Med</i> <b>15</b>(1):6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28065164 28065164]; doi: [https://dx.doi.org/10.1186/s12916-016-0770-8 10.1186/s12916-016-0770-8]; GPMDB: [http://gpmdb.org/data/keyword/28065164 80]. |
+ | #Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C, (2016) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." <i>Chemistry</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28071820 28071820]; doi: [https://dx.doi.org/10.1002/chem.201604516 10.1002/chem.201604516]; GPMDB: [http://gpmdb.org/data/keyword/28071820 6]. | ||
+ | #Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 521]. | ||
+ | #Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. |
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 January 29, 2017.