Line 24: | Line 24: | ||
==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 | + | 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 October 2, 2016. |
+ | #Scott N, Sutton J, Gray C, (1989) "Morphometric diagnosis of serous effusions: refinement of differences between benign and malignant cases by use of outlying values and larger sample size." <i>J Clin Pathol</i> <b>42</b>(6):607–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2738165 2738165]; GPMDB: [http://gpmdb.org/data/keyword/2738165 1]. | ||
#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]. | ||
#Liu T, Qian WJ, Strittmatter EF, Camp DG 2nd, Anderson GA, Thrall BD, Smith RD, (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." <i>Anal Chem</i> <b>76</b>(18):5345–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [http://gpmdb.org/data/keyword/15362891 6]. | #Liu T, Qian WJ, Strittmatter EF, Camp DG 2nd, Anderson GA, Thrall BD, Smith RD, (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." <i>Anal Chem</i> <b>76</b>(18):5345–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [http://gpmdb.org/data/keyword/15362891 6]. | ||
Line 993: | Line 994: | ||
#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 834]. |
#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]. | ||
Line 1,237: | Line 1,238: | ||
#Carabetta VJ, Greco TM, Tanner AW, Cristea IM, Dubnau D, (2016) "Temporal Regulation of the <i>Bacillus subtilis</i> Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth." <i>mSystems</i> <b>1</b>(3):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27376153 27376153]; doi: [https://dx.doi.org/10.1128/mSystems.00005-16 10.1128/mSystems.00005-16]; GPMDB: [http://gpmdb.org/data/keyword/27376153 30]. | #Carabetta VJ, Greco TM, Tanner AW, Cristea IM, Dubnau D, (2016) "Temporal Regulation of the <i>Bacillus subtilis</i> Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth." <i>mSystems</i> <b>1</b>(3):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27376153 27376153]; doi: [https://dx.doi.org/10.1128/mSystems.00005-16 10.1128/mSystems.00005-16]; GPMDB: [http://gpmdb.org/data/keyword/27376153 30]. | ||
#Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A, (2016) "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila." <i>Nat Commun</i> <b>7</b>:12128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27378189 27378189]; doi: [https://dx.doi.org/10.1038/ncomms12128 10.1038/ncomms12128]; GPMDB: [http://gpmdb.org/data/keyword/27378189 25]. | #Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A, (2016) "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila." <i>Nat Commun</i> <b>7</b>:12128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27378189 27378189]; doi: [https://dx.doi.org/10.1038/ncomms12128 10.1038/ncomms12128]; GPMDB: [http://gpmdb.org/data/keyword/27378189 25]. | ||
+ | #Barasa BA, van Oirschot BA, Bianchi P, van Solinge WW, Heck AJ, van Wijk R, Slijper M, (2016) "Proteomics reveals reduced expression of transketolase in pyrimidine 5'-nucleotidase deficient patients." <i>Proteomics Clin Appl</i> <b>10</b>(8):859–69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27381654 27381654]; doi: [https://dx.doi.org/10.1002/prca.201500130 10.1002/prca.201500130]; GPMDB: [http://gpmdb.org/data/keyword/27381654 1]. | ||
#Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grünewald K, Shepherd A, Topf M, (2016) "HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1." <i>Mol Cell Proteomics</i> <b>15</b>(9):2939–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27384951 27384951]; doi: [https://dx.doi.org/10.1074/mcp.M116.058552 10.1074/mcp.M116.058552]; GPMDB: [http://gpmdb.org/data/keyword/27384951 19]. | #Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grünewald K, Shepherd A, Topf M, (2016) "HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1." <i>Mol Cell Proteomics</i> <b>15</b>(9):2939–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27384951 27384951]; doi: [https://dx.doi.org/10.1074/mcp.M116.058552 10.1074/mcp.M116.058552]; GPMDB: [http://gpmdb.org/data/keyword/27384951 19]. | ||
#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]. | ||
Line 1,258: | Line 1,260: | ||
#Soderholm S, Kainov DE, Ohman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA, (2016) "Phosphoproteomics to characterize host response during influenza A virus infection of human macrophages." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27486199 27486199]; doi: [https://dx.doi.org/10.1074/mcp.M116.057984 10.1074/mcp.M116.057984]; GPMDB: [http://gpmdb.org/data/keyword/27486199 20]. | #Soderholm S, Kainov DE, Ohman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA, (2016) "Phosphoproteomics to characterize host response during influenza A virus infection of human macrophages." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27486199 27486199]; doi: [https://dx.doi.org/10.1074/mcp.M116.057984 10.1074/mcp.M116.057984]; GPMDB: [http://gpmdb.org/data/keyword/27486199 20]. | ||
#Deslyper G, Colgan TJ, Cooper AJ, Holland CV, Carolan JC, (2016) "A Proteomic Investigation of Hepatic Resistance to Ascaris in a Murine Model." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004837; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27490109 27490109]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004837 10.1371/journal.pntd.0004837]; GPMDB: [http://gpmdb.org/data/keyword/27490109 12]. | #Deslyper G, Colgan TJ, Cooper AJ, Holland CV, Carolan JC, (2016) "A Proteomic Investigation of Hepatic Resistance to Ascaris in a Murine Model." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004837; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27490109 27490109]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004837 10.1371/journal.pntd.0004837]; GPMDB: [http://gpmdb.org/data/keyword/27490109 12]. | ||
- | #Peltier J, Roperch JP, Audebert S, Borg JP, Camoin L, (2016) "Quantitative proteomic analysis exploring progression of colorectal cancer: Modulation of the serpin family." <i>J Proteomics</i> <b>148</b>:139– | + | #Peltier J, Roperch JP, Audebert S, Borg JP, Camoin L, (2016) "Quantitative proteomic analysis exploring progression of colorectal cancer: Modulation of the serpin family." <i>J Proteomics</i> <b>148</b>:139–48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27492143 27492143]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.031 10.1016/j.jprot.2016.07.031]; GPMDB: [http://gpmdb.org/data/keyword/27492143 2]. |
#Roberts AJ, Fairlamb AH, (2016) "The N-myristoylome of Trypanosoma cruzi." <i>Sci Rep</i> <b>6</b>:31078; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27492267 27492267]; doi: [https://dx.doi.org/10.1038/srep31078 10.1038/srep31078]; GPMDB: [http://gpmdb.org/data/keyword/27492267 12]. | #Roberts AJ, Fairlamb AH, (2016) "The N-myristoylome of Trypanosoma cruzi." <i>Sci Rep</i> <b>6</b>:31078; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27492267 27492267]; doi: [https://dx.doi.org/10.1038/srep31078 10.1038/srep31078]; GPMDB: [http://gpmdb.org/data/keyword/27492267 12]. | ||
#Dubois ML, Bastin C, Lévesque D, Boisvert FM, (2016) "Comprehensive Characterization of Minichromosome Maintenance Complex (MCM) Protein Interactions Using Affinity and Proximity Purifications Coupled to Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(9):2924–34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27494197 27494197]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01081 10.1021/acs.jproteome.5b01081]; GPMDB: [http://gpmdb.org/data/keyword/27494197 109]. | #Dubois ML, Bastin C, Lévesque D, Boisvert FM, (2016) "Comprehensive Characterization of Minichromosome Maintenance Complex (MCM) Protein Interactions Using Affinity and Proximity Purifications Coupled to Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(9):2924–34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27494197 27494197]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01081 10.1021/acs.jproteome.5b01081]; GPMDB: [http://gpmdb.org/data/keyword/27494197 109]. | ||
- | #Lachén-Montes M, González-Morales A, de Morentin XM, Pérez-Valderrama E, Ausín K, Zelaya MV, Serna A, Aso E, Ferrer I, Fernández-Irigoyen J, Santamaría E, (2016) "An early dysregulation of FAK and MEK/ERK signaling pathways precedes the β-amyloid deposition in the olfactory bulb of APP/PS1 mouse model of Alzheimer's disease." <i>J Proteomics</i> <b>148</b>:149– | + | #Lachén-Montes M, González-Morales A, de Morentin XM, Pérez-Valderrama E, Ausín K, Zelaya MV, Serna A, Aso E, Ferrer I, Fernández-Irigoyen J, Santamaría E, (2016) "An early dysregulation of FAK and MEK/ERK signaling pathways precedes the β-amyloid deposition in the olfactory bulb of APP/PS1 mouse model of Alzheimer's disease." <i>J Proteomics</i> <b>148</b>:149–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27498392 27498392]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.032 10.1016/j.jprot.2016.07.032]; GPMDB: [http://gpmdb.org/data/keyword/27498392 20]. |
#Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM, (2016) "Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer." <i>Cell</i> <b>166</b>(4):1041–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27499020 27499020]; doi: [https://dx.doi.org/10.1016/j.cell.2016.07.007 10.1016/j.cell.2016.07.007]; GPMDB: [http://gpmdb.org/data/keyword/27499020 69]. | #Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM, (2016) "Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer." <i>Cell</i> <b>166</b>(4):1041–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27499020 27499020]; doi: [https://dx.doi.org/10.1016/j.cell.2016.07.007 10.1016/j.cell.2016.07.007]; GPMDB: [http://gpmdb.org/data/keyword/27499020 69]. | ||
#Marino F, Mommen GP, Jeko A, Meiring HD, van Gaans-van den Brink JA, Scheltema RA, van Els CA, Heck AJ, (2016) "Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27503676 27503676]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00528 10.1021/acs.jproteome.6b00528]; GPMDB: [http://gpmdb.org/data/keyword/27503676 31]. | #Marino F, Mommen GP, Jeko A, Meiring HD, van Gaans-van den Brink JA, Scheltema RA, van Els CA, Heck AJ, (2016) "Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27503676 27503676]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00528 10.1021/acs.jproteome.6b00528]; GPMDB: [http://gpmdb.org/data/keyword/27503676 31]. | ||
Line 1,272: | Line 1,274: | ||
#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]. | ||
- | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 | + | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 5346]. |
+ | #He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [http://gpmdb.org/data/keyword/27554994 34]. | ||
+ | #Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [http://gpmdb.org/data/keyword/27556644 2]. | ||
+ | #Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [http://gpmdb.org/data/keyword/27557128 6]. | ||
#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(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; 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]. | #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(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; 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]. | ||
#Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-Mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-Transcriptional Level." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. | #Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-Mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-Transcriptional Level." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. |
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 (1,245 publications) was current, as of October 2, 2016.