Line 25: | Line 25: | ||
==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 February 5, 2017. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
Line 1,420: | Line 1,420: | ||
#Rougemont B, Bontemps Gallo S, Ayciriex S, Carriere R, Hondermarck H, Lacroix JM, Le Blanc JC, Lemoine J, (2016) "Scout-MRM: multiplexed targeted mass spectrometry-based assay without retention time scheduling exemplified by Dickeya dadantii proteomic analysis during plant infection." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28029036 28029036]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b03201 10.1021/acs.analchem.6b03201]; GPMDB: [http://gpmdb.org/data/keyword/28029036 8]. | #Rougemont B, Bontemps Gallo S, Ayciriex S, Carriere R, Hondermarck H, Lacroix JM, Le Blanc JC, Lemoine J, (2016) "Scout-MRM: multiplexed targeted mass spectrometry-based assay without retention time scheduling exemplified by Dickeya dadantii proteomic analysis during plant infection." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28029036 28029036]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b03201 10.1021/acs.analchem.6b03201]; GPMDB: [http://gpmdb.org/data/keyword/28029036 8]. | ||
#Hickox AE, Wong AC, Pak K, Strojny C, Ramirez M, Yates JR Rd, Ryan AF, Savas JN, (2016) "Global Analysis of Protein Expression of Inner Ear Hair Cells." <i>J Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28039372 28039372]; doi: [https://dx.doi.org/10.1523/JNEUROSCI.2267-16.2016 10.1523/JNEUROSCI.2267-16.2016]; GPMDB: [http://gpmdb.org/data/keyword/28039372 71]. | #Hickox AE, Wong AC, Pak K, Strojny C, Ramirez M, Yates JR Rd, Ryan AF, Savas JN, (2016) "Global Analysis of Protein Expression of Inner Ear Hair Cells." <i>J Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28039372 28039372]; doi: [https://dx.doi.org/10.1523/JNEUROSCI.2267-16.2016 10.1523/JNEUROSCI.2267-16.2016]; GPMDB: [http://gpmdb.org/data/keyword/28039372 71]. | ||
- | #Hansson KT, Skillbäck T, Pernevik E, Kern S, Portelius E, Höglund K, Brinkmalm G, Holmén-Larsson J, Blennow K, Zetterberg H, Gobom J, (2017) "Expanding the cerebrospinal fluid endopeptidome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28044435 28044435]; doi: [https://dx.doi.org/10.1002/pmic.201600384 10.1002/pmic.201600384]; GPMDB: [http://gpmdb.org/data/keyword/28044435 | + | #Hansson KT, Skillbäck T, Pernevik E, Kern S, Portelius E, Höglund K, Brinkmalm G, Holmén-Larsson J, Blennow K, Zetterberg H, Gobom J, (2017) "Expanding the cerebrospinal fluid endopeptidome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28044435 28044435]; doi: [https://dx.doi.org/10.1002/pmic.201600384 10.1002/pmic.201600384]; GPMDB: [http://gpmdb.org/data/keyword/28044435 36]. |
#Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR, (2017) "Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics." <i>Cell Rep</i> <b>18</b>(1):237–247; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052253 28052253]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.013 10.1016/j.celrep.2016.12.013]; GPMDB: [http://gpmdb.org/data/keyword/28052253 128]. | #Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR, (2017) "Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics." <i>Cell Rep</i> <b>18</b>(1):237–247; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052253 28052253]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.013 10.1016/j.celrep.2016.12.013]; GPMDB: [http://gpmdb.org/data/keyword/28052253 128]. | ||
#Cristobal A, van den Toorn HW, van de Wetering M, Clevers H, Heck AJ, Mohammed S, (2017) "Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer." <i>Cell Rep</i> <b>18</b>(1):263–274; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052255 28052255]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.016 10.1016/j.celrep.2016.12.016]; GPMDB: [http://gpmdb.org/data/keyword/28052255 175]. | #Cristobal A, van den Toorn HW, van de Wetering M, Clevers H, Heck AJ, Mohammed S, (2017) "Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer." <i>Cell Rep</i> <b>18</b>(1):263–274; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052255 28052255]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.016 10.1016/j.celrep.2016.12.016]; GPMDB: [http://gpmdb.org/data/keyword/28052255 175]. | ||
#Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | #Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | ||
#Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28058811 28058811]; doi: [https://dx.doi.org/10.1002/pmic.201600213 10.1002/pmic.201600213]; GPMDB: [http://gpmdb.org/data/keyword/28058811 70]. | #Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28058811 28058811]; doi: [https://dx.doi.org/10.1002/pmic.201600213 10.1002/pmic.201600213]; GPMDB: [http://gpmdb.org/data/keyword/28058811 70]. | ||
- | #Clotet S, Soler MJ, Riera M, Pascual J, Fang F, Zhou J, Batruch I, Vasiliou SK, Dimitromanolakis A, Barrios C, Diamandis E, Scholey J, Konvalinka A, (2017) "SILAC-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062795 28062795]; doi: [https://dx.doi.org/10.1074/mcp.M116.061903 10.1074/mcp.M116.061903]; GPMDB: [http://gpmdb.org/data/keyword/28062795 | + | #Clotet S, Soler MJ, Riera M, Pascual J, Fang F, Zhou J, Batruch I, Vasiliou SK, Dimitromanolakis A, Barrios C, Diamandis E, Scholey J, Konvalinka A, (2017) "SILAC-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062795 28062795]; doi: [https://dx.doi.org/10.1074/mcp.M116.061903 10.1074/mcp.M116.061903]; GPMDB: [http://gpmdb.org/data/keyword/28062795 11]. |
#Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062796 28062796]; doi: [https://dx.doi.org/10.1074/mcp.M116.063511 10.1074/mcp.M116.063511]; GPMDB: [http://gpmdb.org/data/keyword/28062796 166]. | #Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062796 28062796]; doi: [https://dx.doi.org/10.1074/mcp.M116.063511 10.1074/mcp.M116.063511]; GPMDB: [http://gpmdb.org/data/keyword/28062796 166]. | ||
+ | #Diaz-Vera J, Palmer S, Hernandez-Fernaud JR, Dornier E, Mitchell LE, Macpherson I, Edwards J, Zanivan S, Norman JC, (2017) "A proteomic approach to identify endosomal cargoes controlling cancer invasiveness." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062852 28062852]; doi: [https://dx.doi.org/10.1242/jcs.190835 10.1242/jcs.190835]; GPMDB: [http://gpmdb.org/data/keyword/28062852 106]. | ||
#Pietzner M, Engelmann B, Kacprowski T, Golchert J, Dirk AL, Hammer E, Iwen KA, Nauck M, Wallaschofski H, Führer D, Münte TF, Friedrich N, Völker U, Homuth G, Brabant G, (2017) "Plasma proteome and metabolome characterization of an experimental human thyrotoxicosis model." <i>BMC Med</i> <b>15</b>(1):6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28065164 28065164]; doi: [https://dx.doi.org/10.1186/s12916-016-0770-8 10.1186/s12916-016-0770-8]; GPMDB: [http://gpmdb.org/data/keyword/28065164 80]. | #Pietzner M, Engelmann B, Kacprowski T, Golchert J, Dirk AL, Hammer E, Iwen KA, Nauck M, Wallaschofski H, Führer D, Münte TF, Friedrich N, Völker U, Homuth G, Brabant G, (2017) "Plasma proteome and metabolome characterization of an experimental human thyrotoxicosis model." <i>BMC Med</i> <b>15</b>(1):6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28065164 28065164]; doi: [https://dx.doi.org/10.1186/s12916-016-0770-8 10.1186/s12916-016-0770-8]; GPMDB: [http://gpmdb.org/data/keyword/28065164 80]. | ||
#Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C, (2016) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." <i>Chemistry</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28071820 28071820]; doi: [https://dx.doi.org/10.1002/chem.201604516 10.1002/chem.201604516]; GPMDB: [http://gpmdb.org/data/keyword/28071820 6]. | #Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C, (2016) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." <i>Chemistry</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28071820 28071820]; doi: [https://dx.doi.org/10.1002/chem.201604516 10.1002/chem.201604516]; GPMDB: [http://gpmdb.org/data/keyword/28071820 6]. | ||
+ | #Xing F, Luan Y, Cai J, Wu S, Mai J, Gu J, Zhang H, Li K, Lin Y, Xiao X, Liang J, Li Y, Chen W, Tan Y, Sheng L, Lu B, Lu W, Gao M, Qiu P, Su X, Yin W, Hu J, Chen Z, Sai K, Wang J, Chen F, Chen Y, Zhu S, Liu D, Cheng S, Xie Z, Zhu W, Yan G, (2017) "The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes." <i>Cell Rep</i> <b>18</b>(2):468–481; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28076790 28076790]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.037 10.1016/j.celrep.2016.12.037]; GPMDB: [http://gpmdb.org/data/keyword/28076790 60]. | ||
#Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 521]. | #Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 521]. | ||
#Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | #Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | ||
+ | #Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | ||
+ | #Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | ||
+ | #Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML, (2017) "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28112733 28112733]; doi: [https://dx.doi.org/10.1038/nsmb.3366 10.1038/nsmb.3366]; GPMDB: [http://gpmdb.org/data/keyword/28112733 185]. | ||
+ | #Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 656]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of February 5, 2017.