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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 | + | 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 June 10, 2018. |
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Tsai CM, Wu HY, Su TH, Kuo CW, Huang HW, Chung CH, Chen CS, Khoo KH, Chen YJ, Lin KI, (2014) "Phosphoproteomic analyses reveal that galectin-1 augments the dynamics of B-cell receptor signaling." <i>J Proteomics</i> <b>103</b>:241–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24704852 24704852]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.03.031 10.1016/j.jprot.2014.03.031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24704852 15]. | #Tsai CM, Wu HY, Su TH, Kuo CW, Huang HW, Chung CH, Chen CS, Khoo KH, Chen YJ, Lin KI, (2014) "Phosphoproteomic analyses reveal that galectin-1 augments the dynamics of B-cell receptor signaling." <i>J Proteomics</i> <b>103</b>:241–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24704852 24704852]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.03.031 10.1016/j.jprot.2014.03.031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24704852 15]. | ||
#MacLean AM, Orlovskis Z, Kowitwanich K, Zdziarska AM, Angenent GC, Immink RG, Hogenhout SA, (2014) "Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner." <i>PLoS Biol</i> <b>12</b>(4):e1001835; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24714165 24714165]; doi: [https://dx.doi.org/10.1371/journal.pbio.1001835 10.1371/journal.pbio.1001835]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24714165 20]. | #MacLean AM, Orlovskis Z, Kowitwanich K, Zdziarska AM, Angenent GC, Immink RG, Hogenhout SA, (2014) "Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner." <i>PLoS Biol</i> <b>12</b>(4):e1001835; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24714165 24714165]; doi: [https://dx.doi.org/10.1371/journal.pbio.1001835 10.1371/journal.pbio.1001835]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24714165 20]. | ||
+ | #Bourdetsky D, Schmelzer CE, Admon A, (2014) "The nature and extent of contributions by defective ribosome products to the HLA peptidome." <i>Proc Natl Acad Sci U S A</i> <b>111</b>(16):E1591–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24715725 24715725]; doi: [https://dx.doi.org/10.1073/pnas.1321902111 10.1073/pnas.1321902111]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24715725 16]. | ||
#Azimi A, Pernemalm M, Frostvik Stolt M, Hansson J, Lehtiö J, Egyházi Brage S, Hertzman Johansson C, (2014) "Proteomics analysis of melanoma metastases: association between S100A13 expression and chemotherapy resistance." <i>Br J Cancer</i> <b>110</b>(10):2489–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24722184 24722184]; doi: [https://dx.doi.org/10.1038/bjc.2014.169 10.1038/bjc.2014.169]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24722184 146]. | #Azimi A, Pernemalm M, Frostvik Stolt M, Hansson J, Lehtiö J, Egyházi Brage S, Hertzman Johansson C, (2014) "Proteomics analysis of melanoma metastases: association between S100A13 expression and chemotherapy resistance." <i>Br J Cancer</i> <b>110</b>(10):2489–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24722184 24722184]; doi: [https://dx.doi.org/10.1038/bjc.2014.169 10.1038/bjc.2014.169]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24722184 146]. | ||
#Svozil J, Hirsch-Hoffmann M, Dudler R, Gruissem W, Baerenfaller K, (2014) "Protein abundance changes and ubiquitylation targets identified after inhibition of the proteasome with syringolin A." <i>Mol Cell Proteomics</i> <b>13</b>(6):1523–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24732913 24732913]; doi: [https://dx.doi.org/10.1074/mcp.M113.036269 10.1074/mcp.M113.036269]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24732913 128]. | #Svozil J, Hirsch-Hoffmann M, Dudler R, Gruissem W, Baerenfaller K, (2014) "Protein abundance changes and ubiquitylation targets identified after inhibition of the proteasome with syringolin A." <i>Mol Cell Proteomics</i> <b>13</b>(6):1523–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24732913 24732913]; doi: [https://dx.doi.org/10.1074/mcp.M113.036269 10.1074/mcp.M113.036269]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24732913 128]. | ||
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#Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28126900 60]. | #Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28126900 60]. | ||
#Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R, (2017) "Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections." <i>PLoS Pathog</i> <b>13</b>(1):e1006151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28129394 28129394]; doi: [https://dx.doi.org/10.1371/journal.ppat.1006151 10.1371/journal.ppat.1006151]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28129394 72]. | #Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R, (2017) "Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections." <i>PLoS Pathog</i> <b>13</b>(1):e1006151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28129394 28129394]; doi: [https://dx.doi.org/10.1371/journal.ppat.1006151 10.1371/journal.ppat.1006151]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28129394 72]. | ||
+ | #Tuveng TR, Hagen LH, Mekasha S, Frank J, Arntzen MØ, Vaaje-Kolstad G, Eijsink VGH, (2017) "Genomic, proteomic and biochemical analysis of the chitinolytic machinery of Serratia marcescens BJL200." <i>Biochim Biophys Acta</i> <b>1865</b>(4):414–421; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28130068 28130068]; doi: [https://dx.doi.org/10.1016/j.bbapap.2017.01.007 10.1016/j.bbapap.2017.01.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28130068 54]. | ||
#Lorenz C, Lesimple P, Bukowiecki R, Zink A, Inak G, Mlody B, Singh M, Semtner M, Mah N, Auré K, Leong M, Zabiegalov O, Lyras EM, Pfiffer V, Fauler B, Eichhorst J, Wiesner B, Huebner N, Priller J, Mielke T, Meierhofer D, Izsvák Z, Meier JC, Bouillaud F, Adjaye J, Schuelke M, Wanker EE, Lombès A, Prigione A, (2017) "Human iPSC-Derived Neural Progenitors Are an Effective Drug Discovery Model for Neurological mtDNA Disorders." <i>Cell Stem Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132834 28132834]; doi: [https://dx.doi.org/10.1016/j.stem.2016.12.013 10.1016/j.stem.2016.12.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28132834 14]. | #Lorenz C, Lesimple P, Bukowiecki R, Zink A, Inak G, Mlody B, Singh M, Semtner M, Mah N, Auré K, Leong M, Zabiegalov O, Lyras EM, Pfiffer V, Fauler B, Eichhorst J, Wiesner B, Huebner N, Priller J, Mielke T, Meierhofer D, Izsvák Z, Meier JC, Bouillaud F, Adjaye J, Schuelke M, Wanker EE, Lombès A, Prigione A, (2017) "Human iPSC-Derived Neural Progenitors Are an Effective Drug Discovery Model for Neurological mtDNA Disorders." <i>Cell Stem Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132834 28132834]; doi: [https://dx.doi.org/10.1016/j.stem.2016.12.013 10.1016/j.stem.2016.12.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28132834 14]. | ||
#Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28132839 120]. | #Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28132839 120]. | ||
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#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/28666451 37]. | ||
+ | #Yu Y, Bekele S, Pieper R, (2017) "Quick 96FASP for high throughput quantitative proteome analysis." <i>J Proteomics</i> <b>166</b>:1–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28669814 28669814]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.06.019 10.1016/j.jprot.2017.06.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28669814 15]. | ||
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/28673085 6]. | #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: [https://gpmdb.thegpm.org/data/keyword/28673085 6]. | ||
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#Wang Q, Lu Q, (2017) "Plasma membrane-derived extracellular microvesicles mediate non-canonical intercellular NOTCH signaling." <i>Nat Commun</i> <b>8</b>(1):709; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28955033 28955033]; doi: [https://dx.doi.org/10.1038/s41467-017-00767-2 10.1038/s41467-017-00767-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28955033 2]. | #Wang Q, Lu Q, (2017) "Plasma membrane-derived extracellular microvesicles mediate non-canonical intercellular NOTCH signaling." <i>Nat Commun</i> <b>8</b>(1):709; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28955033 28955033]; doi: [https://dx.doi.org/10.1038/s41467-017-00767-2 10.1038/s41467-017-00767-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28955033 2]. | ||
#Triana S, de Cock H, Ohm RA, Danies G, Wösten HAB, Restrepo S, González Barrios AF, Celis A, (2017) "Lipid Metabolic Versatility in <i>Malassezia</i> spp. Yeasts Studied through Metabolic Modeling." <i>Front Microbiol</i> <b>8</b>:1772; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959251 28959251]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01772 10.3389/fmicb.2017.01772]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28959251 37]. | #Triana S, de Cock H, Ohm RA, Danies G, Wösten HAB, Restrepo S, González Barrios AF, Celis A, (2017) "Lipid Metabolic Versatility in <i>Malassezia</i> spp. Yeasts Studied through Metabolic Modeling." <i>Front Microbiol</i> <b>8</b>:1772; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959251 28959251]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01772 10.3389/fmicb.2017.01772]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28959251 37]. | ||
+ | #Megger DA, Philipp J, Le-Trilling VTK, Sitek B, Trilling M, (2017) "Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression." <i>Front Immunol</i> <b>8</b>:1139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959263 28959263]; doi: [https://dx.doi.org/10.3389/fimmu.2017.01139 10.3389/fimmu.2017.01139]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28959263 114]. | ||
#Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P, (2017) "Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959888 28959888]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00340 10.1021/acs.jproteome.7b00340]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28959888 63]. | #Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P, (2017) "Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959888 28959888]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00340 10.1021/acs.jproteome.7b00340]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28959888 63]. | ||
#Stadlmann J, Taubenschmid J, Wenzel D, Gattinger A, Dürnberger G, Dusberger F, Elling U, Mach L, Mechtler K, Penninger JM, (2017) "Comparative glycoproteomics of stem cells identifies new players in ricin toxicity." <i>Nature</i> <b>549</b>(7673):538–542; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959962 28959962]; doi: [https://dx.doi.org/10.1038/nature24015 10.1038/nature24015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28959962 1]. | #Stadlmann J, Taubenschmid J, Wenzel D, Gattinger A, Dürnberger G, Dusberger F, Elling U, Mach L, Mechtler K, Penninger JM, (2017) "Comparative glycoproteomics of stem cells identifies new players in ricin toxicity." <i>Nature</i> <b>549</b>(7673):538–542; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959962 28959962]; doi: [https://dx.doi.org/10.1038/nature24015 10.1038/nature24015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28959962 1]. | ||
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#Rosting C, Yu J, Cooper HJ, (2018) "High Field Asymmetric Waveform Ion Mobility Spectrometry in Nontargeted Bottom-up Proteomics of Dried Blood Spots." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707944 29707944]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00746 10.1021/acs.jproteome.7b00746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707944 42]. | #Rosting C, Yu J, Cooper HJ, (2018) "High Field Asymmetric Waveform Ion Mobility Spectrometry in Nontargeted Bottom-up Proteomics of Dried Blood Spots." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707944 29707944]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00746 10.1021/acs.jproteome.7b00746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707944 42]. | ||
#Chen X, Yu C, Gao J, Zhu H, Cui B, Zhang T, Zhou Y, Liu Q, He H, Xiao R, Huang R, Xie H, Gao D, Zhou H, (2018) "A novel USP9X substrate TTK contributes to tumorigenesis in non-small-cell lung cancer." <i>Theranostics</i> <b>8</b>(9):2348–2360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29721084 29721084]; doi: [https://dx.doi.org/10.7150/thno.22901 10.7150/thno.22901]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29721084 1]. | #Chen X, Yu C, Gao J, Zhu H, Cui B, Zhang T, Zhou Y, Liu Q, He H, Xiao R, Huang R, Xie H, Gao D, Zhou H, (2018) "A novel USP9X substrate TTK contributes to tumorigenesis in non-small-cell lung cancer." <i>Theranostics</i> <b>8</b>(9):2348–2360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29721084 29721084]; doi: [https://dx.doi.org/10.7150/thno.22901 10.7150/thno.22901]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29721084 1]. | ||
+ | #Van Quickelberghe E, Martens A, Goeminne LJE, Clement L, van Loo G, Gevaert K, (2018) "Identification of Immune-Responsive Gene 1 (IRG1) as a Target of A20." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29733654 29733654]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00139 10.1021/acs.jproteome.8b00139]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29733654 30]. | ||
#Meier F, Geyer PE, Virreira Winter S, Cox J, Mann M, (2018) "BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29735998 29735998]; doi: [https://dx.doi.org/10.1038/s41592-018-0003-5 10.1038/s41592-018-0003-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29735998 60]. | #Meier F, Geyer PE, Virreira Winter S, Cox J, Mann M, (2018) "BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29735998 29735998]; doi: [https://dx.doi.org/10.1038/s41592-018-0003-5 10.1038/s41592-018-0003-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29735998 60]. | ||
#Seltmann K, Meyer M, Sulcova J, Kockmann T, Wehkamp U, Weidinger S, Auf dem Keller U, Werner S, (2018) "Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress." <i>Sci Transl Med</i> <b>10</b>(440):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29743348 29743348]; doi: [https://dx.doi.org/10.1126/scitranslmed.aao4650 10.1126/scitranslmed.aao4650]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29743348 24]. | #Seltmann K, Meyer M, Sulcova J, Kockmann T, Wehkamp U, Weidinger S, Auf dem Keller U, Werner S, (2018) "Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress." <i>Sci Transl Med</i> <b>10</b>(440):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29743348 29743348]; doi: [https://dx.doi.org/10.1126/scitranslmed.aao4650 10.1126/scitranslmed.aao4650]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29743348 24]. | ||
+ | #Gaviard C, Broutin I, Cosette P, De E, Jouenne T, Hardouin J, (2018) "Lysine succinylation and acetylation in Pseudomonas aeruginosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29770699 29770699]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00210 10.1021/acs.jproteome.8b00210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29770699 24]. | ||
+ | #Di Lorenzo G, Voltolini Velho R, Winter D, Thelen M, Ahmadi S, Schweizer M, De Pace R, Cornils K, Yorgan TA, Grüb S, Hermans-Borgmeyer I, Schinke T, Müller-Loennies S, Braulke T, Pohl S, (2018) "Lysosomal proteome and secretome analysis identifies missorted enzymes and their non-degraded substrates in mucolipidosis III mouse cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29773673 29773673]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000720 10.1074/mcp.RA118.000720]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29773673 30]. | ||
+ | #Wang H, Cheng Q, Li X, Hu F, Han L, Zhang H, Li L, Ge J, Ying X, Guo X, Wang Q, (2018) "Loss of TIGAR induces oxidative stress and meiotic defects in oocytes from obese mice." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29776966 29776966]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000620 10.1074/mcp.RA118.000620]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29776966 9]. | ||
+ | #Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, Rammensee HG, Stevanovic S, Haen SP, (2018) "Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29789417 29789417]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-17-1745 10.1158/0008-5472.CAN-17-1745]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29789417 530]. | ||
+ | #Souquet B, Freed E, Berto A, Andric V, Audugé N, Reina-San-Martin B, Lacy E, Doye V, (2018) "Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells." <i>Cell Rep</i> <b>23</b>(8):2443–2454; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29791854 29791854]; doi: [https://dx.doi.org/10.1016/j.celrep.2018.04.070 10.1016/j.celrep.2018.04.070]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29791854 18]. | ||
+ | #Muller L, Fornecker L, Chion M, Van Dorsselaer A, Cianférani S, Rabilloud T, Carapito C, (2018) "Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics." <i>Sci Rep</i> <b>8</b>(1):8260; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29844437 29844437]; doi: [https://dx.doi.org/10.1038/s41598-018-26600-4 10.1038/s41598-018-26600-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29844437 40]. | ||
+ | #Mohammad I, Nousiainen K, Bhosale SD, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z, (2018) "Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells." <i>PLoS Biol</i> <b>16</b>(5):e2004194; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29851958 29851958]; doi: [https://dx.doi.org/10.1371/journal.pbio.2004194 10.1371/journal.pbio.2004194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29851958 45]. | ||
+ | #Marín E, Haesaert A, Padilla L, Adán J, Hernáez ML, Monteoliva L, Gil C, (2018) "Unraveling <i>Gardnerella vaginalis</i> Surface Proteins Using Cell Shaving Proteomics." <i>Front Microbiol</i> <b>9</b>:975; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29867878 29867878]; doi: [https://dx.doi.org/10.3389/fmicb.2018.00975 10.3389/fmicb.2018.00975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29867878 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 be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
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 June 10, 2018.