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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 25, 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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#Jerebtsova M, Kumari N, Obuhkov Y, Nekhai S, (2012) "Adenoviral E4 gene stimulates secretion of pigmental epithelium derived factor (PEDF) that maintains long-term survival of human glomerulus-derived endothelial cells." <i>Mol Cell Proteomics</i> <b>11</b>(11):1378–88; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22915824 22915824]; doi: [https://dx.doi.org/10.1074/mcp.M112.020313 10.1074/mcp.M112.020313]; GPMDB: [http://gpmdb.org/data/keyword/22915824 20]. | #Jerebtsova M, Kumari N, Obuhkov Y, Nekhai S, (2012) "Adenoviral E4 gene stimulates secretion of pigmental epithelium derived factor (PEDF) that maintains long-term survival of human glomerulus-derived endothelial cells." <i>Mol Cell Proteomics</i> <b>11</b>(11):1378–88; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22915824 22915824]; doi: [https://dx.doi.org/10.1074/mcp.M112.020313 10.1074/mcp.M112.020313]; GPMDB: [http://gpmdb.org/data/keyword/22915824 20]. | ||
#Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W, (2012) "Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit." <i>Mol Syst Biol</i> <b>8</b>:606; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22929616 22929616]; doi: [https://dx.doi.org/10.1038/msb.2012.39 10.1038/msb.2012.39]; GPMDB: [http://gpmdb.org/data/keyword/22929616 24]. | #Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W, (2012) "Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit." <i>Mol Syst Biol</i> <b>8</b>:606; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22929616 22929616]; doi: [https://dx.doi.org/10.1038/msb.2012.39 10.1038/msb.2012.39]; GPMDB: [http://gpmdb.org/data/keyword/22929616 24]. | ||
- | #Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A, (2012) "A census of human soluble protein complexes." <i>Cell</i> <b>150</b>(5):1068–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22939629 22939629]; doi: [https://dx.doi.org/10.1016/j.cell.2012.08.011 10.1016/j.cell.2012.08.011]; GPMDB: [http://gpmdb.org/data/keyword/22939629 | + | #Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A, (2012) "A census of human soluble protein complexes." <i>Cell</i> <b>150</b>(5):1068–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22939629 22939629]; doi: [https://dx.doi.org/10.1016/j.cell.2012.08.011 10.1016/j.cell.2012.08.011]; GPMDB: [http://gpmdb.org/data/keyword/22939629 2355]. |
#MacDonald ML, Ciccimaro E, Prakash A, Banerjee A, Seeholzer SH, Blair IA, Hahn CG, (2012) "Biochemical fractionation and stable isotope dilution liquid chromatography-mass spectrometry for targeted and microdomain-specific protein quantification in human postmortem brain tissue." <i>Mol Cell Proteomics</i> <b>11</b>(12):1670–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22942359 22942359]; doi: [https://dx.doi.org/10.1074/mcp.M112.021766 10.1074/mcp.M112.021766]; GPMDB: [http://gpmdb.org/data/keyword/22942359 14]. | #MacDonald ML, Ciccimaro E, Prakash A, Banerjee A, Seeholzer SH, Blair IA, Hahn CG, (2012) "Biochemical fractionation and stable isotope dilution liquid chromatography-mass spectrometry for targeted and microdomain-specific protein quantification in human postmortem brain tissue." <i>Mol Cell Proteomics</i> <b>11</b>(12):1670–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22942359 22942359]; doi: [https://dx.doi.org/10.1074/mcp.M112.021766 10.1074/mcp.M112.021766]; GPMDB: [http://gpmdb.org/data/keyword/22942359 14]. | ||
#Vögtle FN, Burkhart JM, Rao S, Gerbeth C, Hinrichs J, Martinou JC, Chacinska A, Sickmann A, Zahedi RP, Meisinger C, (2012) "Intermembrane space proteome of yeast mitochondria." <i>Mol Cell Proteomics</i> <b>11</b>(12):1840–52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22984289 22984289]; doi: [https://dx.doi.org/10.1074/mcp.M112.021105 10.1074/mcp.M112.021105]; GPMDB: [http://gpmdb.org/data/keyword/22984289 30]. | #Vögtle FN, Burkhart JM, Rao S, Gerbeth C, Hinrichs J, Martinou JC, Chacinska A, Sickmann A, Zahedi RP, Meisinger C, (2012) "Intermembrane space proteome of yeast mitochondria." <i>Mol Cell Proteomics</i> <b>11</b>(12):1840–52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22984289 22984289]; doi: [https://dx.doi.org/10.1074/mcp.M112.021105 10.1074/mcp.M112.021105]; GPMDB: [http://gpmdb.org/data/keyword/22984289 30]. | ||
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#Masuishi Y, Kimura Y, Arakawa N, Hirano H, (2016) "Data for identification of GPI-anchored peptides and ω-sites in cancer cell lines." <i>Data Brief</i> <b>7</b>:1302–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141528 27141528]; doi: [https://dx.doi.org/10.1016/j.dib.2016.04.001 10.1016/j.dib.2016.04.001]; GPMDB: [http://gpmdb.org/data/keyword/27141528 42]. | #Masuishi Y, Kimura Y, Arakawa N, Hirano H, (2016) "Data for identification of GPI-anchored peptides and ω-sites in cancer cell lines." <i>Data Brief</i> <b>7</b>:1302–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141528 27141528]; doi: [https://dx.doi.org/10.1016/j.dib.2016.04.001 10.1016/j.dib.2016.04.001]; GPMDB: [http://gpmdb.org/data/keyword/27141528 42]. | ||
#Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA Jr, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM, (2016) "The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids." <i>Mol Cell Proteomics</i> <b>15</b>(7):2366–78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27143409 27143409]; doi: [https://dx.doi.org/10.1074/mcp.M115.056036 10.1074/mcp.M115.056036]; GPMDB: [http://gpmdb.org/data/keyword/27143409 28]. | #Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA Jr, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM, (2016) "The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids." <i>Mol Cell Proteomics</i> <b>15</b>(7):2366–78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27143409 27143409]; doi: [https://dx.doi.org/10.1074/mcp.M115.056036 10.1074/mcp.M115.056036]; GPMDB: [http://gpmdb.org/data/keyword/27143409 28]. | ||
- | #Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | + | #Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i> <b>7</b>(23):33627–48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. |
#Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | #Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | ||
#Packialakshmi B, Liyanage R, Lay JO Jr, Okimoto R, Rath NC, (2016) "Proteomic Changes in the Plasma of Broiler Chickens with Femoral Head Necrosis." <i>Biomark Insights</i> <b>11</b>:55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27147818 27147818]; doi: [https://dx.doi.org/10.4137/BMI.S38291 10.4137/BMI.S38291]; GPMDB: [http://gpmdb.org/data/keyword/27147818 6]. | #Packialakshmi B, Liyanage R, Lay JO Jr, Okimoto R, Rath NC, (2016) "Proteomic Changes in the Plasma of Broiler Chickens with Femoral Head Necrosis." <i>Biomark Insights</i> <b>11</b>:55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27147818 27147818]; doi: [https://dx.doi.org/10.4137/BMI.S38291 10.4137/BMI.S38291]; GPMDB: [http://gpmdb.org/data/keyword/27147818 6]. | ||
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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]. | ||
- | #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 2652]. |
- | #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 | + | #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]. |
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 September 25, 2016.