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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 (1,245 publications) was current, as of September | + | 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 (1,245 publications) was current, as of September 11, 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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#Aurass P, Gerlach T, Becher D, Voigt B, Karste S, Bernhardt J, Riedel K, Hecker M, Flieger A, (2016) "Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors." <i>Mol Cell Proteomics</i> <b>15</b>(1):177–200; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26545400 26545400]; doi: [https://dx.doi.org/10.1074/mcp.M115.053579 10.1074/mcp.M115.053579]; GPMDB: [http://gpmdb.org/data/keyword/26545400 209]. | #Aurass P, Gerlach T, Becher D, Voigt B, Karste S, Bernhardt J, Riedel K, Hecker M, Flieger A, (2016) "Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors." <i>Mol Cell Proteomics</i> <b>15</b>(1):177–200; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26545400 26545400]; doi: [https://dx.doi.org/10.1074/mcp.M115.053579 10.1074/mcp.M115.053579]; GPMDB: [http://gpmdb.org/data/keyword/26545400 209]. | ||
#Bensaddek D, Narayan V, Nicolas A, Murillo AB, Gartner A, Kenyon CJ, Lamond AI, (2016) "Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level." <i>Proteomics</i> <b>16</b>(3):381–92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26552604 26552604]; doi: [https://dx.doi.org/10.1002/pmic.201500264 10.1002/pmic.201500264]; GPMDB: [http://gpmdb.org/data/keyword/26552604 40]. | #Bensaddek D, Narayan V, Nicolas A, Murillo AB, Gartner A, Kenyon CJ, Lamond AI, (2016) "Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level." <i>Proteomics</i> <b>16</b>(3):381–92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26552604 26552604]; doi: [https://dx.doi.org/10.1002/pmic.201500264 10.1002/pmic.201500264]; GPMDB: [http://gpmdb.org/data/keyword/26552604 40]. | ||
- | #Dimayacyac-Esleta BR, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ, (2015) "Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling." <i>Anal Chem</i> <b>87</b>(24):12016–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26554430 26554430]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b03639 10.1021/acs.analchem.5b03639]; GPMDB: [http://gpmdb.org/data/keyword/26554430 | + | #Dimayacyac-Esleta BR, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ, (2015) "Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling." <i>Anal Chem</i> <b>87</b>(24):12016–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26554430 26554430]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b03639 10.1021/acs.analchem.5b03639]; GPMDB: [http://gpmdb.org/data/keyword/26554430 14]. |
#Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D, (2016) "Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication." <i>Mol Cell Proteomics</i> <b>15</b>(1):218–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560065 26560065]; doi: [https://dx.doi.org/10.1074/mcp.M115.051854 10.1074/mcp.M115.051854]; GPMDB: [http://gpmdb.org/data/keyword/26560065 150]. | #Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D, (2016) "Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication." <i>Mol Cell Proteomics</i> <b>15</b>(1):218–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560065 26560065]; doi: [https://dx.doi.org/10.1074/mcp.M115.051854 10.1074/mcp.M115.051854]; GPMDB: [http://gpmdb.org/data/keyword/26560065 150]. | ||
#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]. | ||
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#De Marchi T, Kuhn E, Dekker LJ, Stingl C, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Luider TM, Foekens JA, Martens JW, Carr SA, Umar A, (2016) "Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera." <i>J Proteome Res</i> <b>15</b>(4):1230–42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26958999 26958999]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01119 10.1021/acs.jproteome.5b01119]; GPMDB: [http://gpmdb.org/data/keyword/26958999 78]. | #De Marchi T, Kuhn E, Dekker LJ, Stingl C, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Luider TM, Foekens JA, Martens JW, Carr SA, Umar A, (2016) "Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera." <i>J Proteome Res</i> <b>15</b>(4):1230–42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26958999 26958999]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01119 10.1021/acs.jproteome.5b01119]; GPMDB: [http://gpmdb.org/data/keyword/26958999 78]. | ||
#Jo DH, Bae J, Chae S, Kim JH, Han JH, Hwang D, Lee SW, Kim JH, (2016) "Quantitative Proteomics Reveals β2 Integrin-mediated Cytoskeletal Rearrangement in Vascular Endothelial Growth Factor (VEGF)-induced Retinal Vascular Hyperpermeability." <i>Mol Cell Proteomics</i> <b>15</b>(5):1681–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26969716 26969716]; doi: [https://dx.doi.org/10.1074/mcp.M115.053249 10.1074/mcp.M115.053249]; GPMDB: [http://gpmdb.org/data/keyword/26969716 72]. | #Jo DH, Bae J, Chae S, Kim JH, Han JH, Hwang D, Lee SW, Kim JH, (2016) "Quantitative Proteomics Reveals β2 Integrin-mediated Cytoskeletal Rearrangement in Vascular Endothelial Growth Factor (VEGF)-induced Retinal Vascular Hyperpermeability." <i>Mol Cell Proteomics</i> <b>15</b>(5):1681–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26969716 26969716]; doi: [https://dx.doi.org/10.1074/mcp.M115.053249 10.1074/mcp.M115.053249]; GPMDB: [http://gpmdb.org/data/keyword/26969716 72]. | ||
+ | #Lau E, Cao Q, Ng DC, Bleakley BJ, Dincer TU, Bot BM, Wang D, Liem DA, Lam MP, Ge J, Ping P, (2016) "A large dataset of protein dynamics in the mammalian heart proteome." <i>Sci Data</i> <b>3</b>:160015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26977904 26977904]; doi: [https://dx.doi.org/10.1038/sdata.2016.15 10.1038/sdata.2016.15]; GPMDB: [http://gpmdb.org/data/keyword/26977904 257]. | ||
#Gallart-Palau X, Lee BS, Adav SS, Qian J, Serra A, Park JE, Lai MK, Chen CP, Kalaria RN, Sze SK, (2016) "Gender differences in white matter pathology and mitochondrial dysfunction in Alzheimer's disease with cerebrovascular disease." <i>Mol Brain</i> <b>9</b>:27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26983404 26983404]; doi: [https://dx.doi.org/10.1186/s13041-016-0205-7 10.1186/s13041-016-0205-7]; GPMDB: [http://gpmdb.org/data/keyword/26983404 10]. | #Gallart-Palau X, Lee BS, Adav SS, Qian J, Serra A, Park JE, Lai MK, Chen CP, Kalaria RN, Sze SK, (2016) "Gender differences in white matter pathology and mitochondrial dysfunction in Alzheimer's disease with cerebrovascular disease." <i>Mol Brain</i> <b>9</b>:27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26983404 26983404]; doi: [https://dx.doi.org/10.1186/s13041-016-0205-7 10.1186/s13041-016-0205-7]; GPMDB: [http://gpmdb.org/data/keyword/26983404 10]. | ||
#Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." <i>Int J Med Microbiol</i> <b>306</b>(3):131–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26996810 26996810]; doi: [https://dx.doi.org/10.1016/j.ijmm.2016.02.004 10.1016/j.ijmm.2016.02.004]; GPMDB: [http://gpmdb.org/data/keyword/26996810 300]. | #Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." <i>Int J Med Microbiol</i> <b>306</b>(3):131–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26996810 26996810]; doi: [https://dx.doi.org/10.1016/j.ijmm.2016.02.004 10.1016/j.ijmm.2016.02.004]; GPMDB: [http://gpmdb.org/data/keyword/26996810 300]. | ||
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#Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 27]. | #Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 27]. | ||
#Madeira JP, Omer H, Alpha-Bazin B, Armengaud J, Duport C, (2016) "Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics." <i>J Proteomics</i> <b>146</b>:25–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27321915 27321915]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.06.022 10.1016/j.jprot.2016.06.022]; GPMDB: [http://gpmdb.org/data/keyword/27321915 26]. | #Madeira JP, Omer H, Alpha-Bazin B, Armengaud J, Duport C, (2016) "Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics." <i>J Proteomics</i> <b>146</b>:25–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27321915 27321915]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.06.022 10.1016/j.jprot.2016.06.022]; GPMDB: [http://gpmdb.org/data/keyword/27321915 26]. | ||
- | #Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. | + | #Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i> <b>16</b>(17):2345–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. |
#Ahrné E, Glatter T, Viganò C, Schubert Cv, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i> <b>15</b>(8):2537–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 41]. | #Ahrné E, Glatter T, Viganò C, Schubert Cv, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i> <b>15</b>(8):2537–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 41]. | ||
#Chaubey PM, Hofstetter L, Roschitzki B, Stieger B, (2016) "Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver." <i>PLoS One</i> <b>11</b>(6):e0158033; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27347675 27347675]; doi: [https://dx.doi.org/10.1371/journal.pone.0158033 10.1371/journal.pone.0158033]; GPMDB: [http://gpmdb.org/data/keyword/27347675 60]. | #Chaubey PM, Hofstetter L, Roschitzki B, Stieger B, (2016) "Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver." <i>PLoS One</i> <b>11</b>(6):e0158033; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27347675 27347675]; doi: [https://dx.doi.org/10.1371/journal.pone.0158033 10.1371/journal.pone.0158033]; GPMDB: [http://gpmdb.org/data/keyword/27347675 60]. | ||
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#Picariello G, Addeo F, Ferranti P, Nocerino R, Paparo L, Passariello A, Dallas DC, Robinson RC, Barile D, Canani RB, (2016) "Antibody-independent identification of bovine milk-derived peptides in breast-milk." <i>Food Funct</i> <b>7</b>(8):3402–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27396729 27396729]; doi: [https://dx.doi.org/10.1039/c6fo00731g 10.1039/c6fo00731g]; GPMDB: [http://gpmdb.org/data/keyword/27396729 12]. | #Picariello G, Addeo F, Ferranti P, Nocerino R, Paparo L, Passariello A, Dallas DC, Robinson RC, Barile D, Canani RB, (2016) "Antibody-independent identification of bovine milk-derived peptides in breast-milk." <i>Food Funct</i> <b>7</b>(8):3402–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27396729 27396729]; doi: [https://dx.doi.org/10.1039/c6fo00731g 10.1039/c6fo00731g]; GPMDB: [http://gpmdb.org/data/keyword/27396729 12]. | ||
#Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i> <b>166</b>(3):664–78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. | #Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i> <b>166</b>(3):664–78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. | ||
- | #Konstantinell A, Bruun JA, Olsen R, Aspar A, Škalko-Basnet N, Sveinbjørnsson B, Moens U, (2016) "Secretomic analysis of extracellular vesicles originating from | + | #Konstantinell A, Bruun JA, Olsen R, Aspar A, Škalko-Basnet N, Sveinbjørnsson B, Moens U, (2016) "Secretomic analysis of extracellular vesicles originating from polyomavirus-negative and polyomavirus-positive Merkel cell carcinoma cell lines." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27402257 27402257]; doi: [https://dx.doi.org/10.1002/pmic.201600223 10.1002/pmic.201600223]; GPMDB: [http://gpmdb.org/data/keyword/27402257 28]. |
#Shraibman B, Kadosh DM, Barnea E, Admon A, (2016) "Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy." <i>Mol Cell Proteomics</i> <b>15</b>(9):3058–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [http://gpmdb.org/data/keyword/27412690 60]. | #Shraibman B, Kadosh DM, Barnea E, Admon A, (2016) "Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy." <i>Mol Cell Proteomics</i> <b>15</b>(9):3058–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [http://gpmdb.org/data/keyword/27412690 60]. | ||
#Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | #Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | ||
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#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>; 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>; 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]. | ||
+ | #Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8<sup>+</sup> T Cells." <i>Immunity</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. |
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.
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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 (1,245 publications) was current, as of September 11, 2016.