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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 October 14, 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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#Courtney DG, Poulsen ET, Kennedy S, Moore JE, Atkinson SD, Maurizi E, Nesbit MA, Moore CB, Enghild JJ, (2015) "Protein Composition of TGFBI-R124C- and TGFBI-R555W-Associated Aggregates Suggests Multiple Mechanisms Leading to Lattice and Granular Corneal Dystrophy." <i>Invest Ophthalmol Vis Sci</i> <b>56</b>(8):4653–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26207300 26207300]; doi: [https://dx.doi.org/10.1167/iovs.15-16922 10.1167/iovs.15-16922]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26207300 39]. | #Courtney DG, Poulsen ET, Kennedy S, Moore JE, Atkinson SD, Maurizi E, Nesbit MA, Moore CB, Enghild JJ, (2015) "Protein Composition of TGFBI-R124C- and TGFBI-R555W-Associated Aggregates Suggests Multiple Mechanisms Leading to Lattice and Granular Corneal Dystrophy." <i>Invest Ophthalmol Vis Sci</i> <b>56</b>(8):4653–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26207300 26207300]; doi: [https://dx.doi.org/10.1167/iovs.15-16922 10.1167/iovs.15-16922]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26207300 39]. | ||
#Díez P, Droste C, Dégano RM, González-Muñoz M, Ibarrola N, Pérez-Andrés M, Garin-Muga A, Segura V, Marko-Varga G, LaBaer J, Orfao A, Corrales FJ, De Las Rivas J, Fuentes M, (2015) "Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3530–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26216070 26216070]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00474 10.1021/acs.jproteome.5b00474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26216070 60]. | #Díez P, Droste C, Dégano RM, González-Muñoz M, Ibarrola N, Pérez-Andrés M, Garin-Muga A, Segura V, Marko-Varga G, LaBaer J, Orfao A, Corrales FJ, De Las Rivas J, Fuentes M, (2015) "Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3530–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26216070 26216070]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00474 10.1021/acs.jproteome.5b00474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26216070 60]. | ||
+ | #Golizeh M, Schneider C, Ohlund LB, Sleno L, (2015) "Dataset from proteomic analysis of rat, mouse, and human liver microsomes and S9 fractions." <i>Data Brief</i> <b>3</b>:95–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26217725 26217725]; doi: [https://dx.doi.org/10.1016/j.dib.2015.02.007 10.1016/j.dib.2015.02.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26217725 4]. | ||
#Berger ST, Ahmed S, Muntel J, Cuevas Polo N, Bachur R, Kentsis A, Steen J, Steen H, (2015) "MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates." <i>Mol Cell Proteomics</i> <b>14</b>(10):2814–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26223766 26223766]; doi: [https://dx.doi.org/10.1074/mcp.O115.049650 10.1074/mcp.O115.049650]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26223766 113]. | #Berger ST, Ahmed S, Muntel J, Cuevas Polo N, Bachur R, Kentsis A, Steen J, Steen H, (2015) "MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates." <i>Mol Cell Proteomics</i> <b>14</b>(10):2814–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26223766 26223766]; doi: [https://dx.doi.org/10.1074/mcp.O115.049650 10.1074/mcp.O115.049650]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26223766 113]. | ||
#Woo J, Han D, Park J, Kim SJ, Kim Y, (2015) "In-depth characterization of the secretome of mouse CNS cell lines by LC-MS/MS without prefractionation." <i>Proteomics</i> <b>15</b>(21):3617–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26227174 26227174]; doi: [https://dx.doi.org/10.1002/pmic.201400623 10.1002/pmic.201400623]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26227174 27]. | #Woo J, Han D, Park J, Kim SJ, Kim Y, (2015) "In-depth characterization of the secretome of mouse CNS cell lines by LC-MS/MS without prefractionation." <i>Proteomics</i> <b>15</b>(21):3617–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26227174 26227174]; doi: [https://dx.doi.org/10.1002/pmic.201400623 10.1002/pmic.201400623]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26227174 27]. | ||
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#O'Loughlin T, Masters TA, Buss F, (2018) "The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467281 29467281]; doi: [https://dx.doi.org/10.15252/embr.201744884 10.15252/embr.201744884]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29467281 34]. | #O'Loughlin T, Masters TA, Buss F, (2018) "The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467281 29467281]; doi: [https://dx.doi.org/10.15252/embr.201744884 10.15252/embr.201744884]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29467281 34]. | ||
#Di Costanzo A, Del Gaudio N, Conte L, Dell'Aversana C, Vermeulen M, de Thé H, Migliaccio A, Nebbioso A, Altucci L, (2018) "The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467492 29467492]; doi: [https://dx.doi.org/10.1038/s41388-018-0143-1 10.1038/s41388-018-0143-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29467492 6]. | #Di Costanzo A, Del Gaudio N, Conte L, Dell'Aversana C, Vermeulen M, de Thé H, Migliaccio A, Nebbioso A, Altucci L, (2018) "The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467492 29467492]; doi: [https://dx.doi.org/10.1038/s41388-018-0143-1 10.1038/s41388-018-0143-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29467492 6]. | ||
+ | #Lee SE, Song J, Bösl K, Müller AC, Vitko D, Bennett KL, Superti-Furga G, Pandey A, Kandasamy RK, Kim MS, (2018) "Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines." <i>Proteomics</i> <b>18</b>(8):e1700386; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29474001 29474001]; doi: [https://dx.doi.org/10.1002/pmic.201700386 10.1002/pmic.201700386]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29474001 200]. | ||
#Chen D, Shen X, Sun L, (2018) "Strong cation exchange-reversed phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry platform with high peak capacity for deep bottom-up proteomics." <i>Anal Chim Acta</i> <b>1012</b>:1–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29475469 29475469]; doi: [https://dx.doi.org/10.1016/j.aca.2018.01.037 10.1016/j.aca.2018.01.037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29475469 2]. | #Chen D, Shen X, Sun L, (2018) "Strong cation exchange-reversed phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry platform with high peak capacity for deep bottom-up proteomics." <i>Anal Chim Acta</i> <b>1012</b>:1–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29475469 29475469]; doi: [https://dx.doi.org/10.1016/j.aca.2018.01.037 10.1016/j.aca.2018.01.037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29475469 2]. | ||
#Hermanns T, Pichlo C, Woiwode I, Klopffleisch K, Witting KF, Ovaa H, Baumann U, Hofmann K, (2018) "A family of unconventional deubiquitinases with modular chain specificity determinants." <i>Nat Commun</i> <b>9</b>(1):799; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29476094 29476094]; doi: [https://dx.doi.org/10.1038/s41467-018-03148-5 10.1038/s41467-018-03148-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29476094 18]. | #Hermanns T, Pichlo C, Woiwode I, Klopffleisch K, Witting KF, Ovaa H, Baumann U, Hofmann K, (2018) "A family of unconventional deubiquitinases with modular chain specificity determinants." <i>Nat Commun</i> <b>9</b>(1):799; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29476094 29476094]; doi: [https://dx.doi.org/10.1038/s41467-018-03148-5 10.1038/s41467-018-03148-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29476094 18]. | ||
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#Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP, (2018) "Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30097533 30097533]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000749 10.1074/mcp.RA118.000749]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30097533 44]. | #Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP, (2018) "Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30097533 30097533]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000749 10.1074/mcp.RA118.000749]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30097533 44]. | ||
#Hwang H, Jeong JE, Lee HK, Yun KN, An HJ, Lee B, Paik YK, Jeong TS, Yee GT, Kim JY, Yoo JS, (2018) "Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30113170 30113170]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00408 10.1021/acs.jproteome.8b00408]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30113170 23]. | #Hwang H, Jeong JE, Lee HK, Yun KN, An HJ, Lee B, Paik YK, Jeong TS, Yee GT, Kim JY, Yoo JS, (2018) "Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30113170 30113170]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00408 10.1021/acs.jproteome.8b00408]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30113170 23]. | ||
+ | #DeLeon-Pennell KY, Mouton AJ, Ero OK, Ma Y, Padmanabhan Iyer R, Flynn ER, Espinoza I, Musani SK, Vasan RS, Hall ME, Fox ER, Lindsey ML, (2018) "LXR/RXR signaling and neutrophil phenotype following myocardial infarction classify sex differences in remodeling." <i>Basic Res Cardiol</i> <b>113</b>(5):40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30132266 30132266]; doi: [https://dx.doi.org/10.1007/s00395-018-0699-5 10.1007/s00395-018-0699-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30132266 120]. | ||
#Weßbecher IM, Hinrichsen I, Funke S, Oellerich T, Plotz G, Zeuzem S, Grus FH, Biondi RM, Brieger A, (2018) "DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)." <i>Mol Carcinog</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30136313 30136313]; doi: [https://dx.doi.org/10.1002/mc.22892 10.1002/mc.22892]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30136313 2]. | #Weßbecher IM, Hinrichsen I, Funke S, Oellerich T, Plotz G, Zeuzem S, Grus FH, Biondi RM, Brieger A, (2018) "DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)." <i>Mol Carcinog</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30136313 30136313]; doi: [https://dx.doi.org/10.1002/mc.22892 10.1002/mc.22892]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30136313 2]. | ||
+ | #Béguin EP, van den Eshof BL, Hoogendijk AJ, Nota B, Mertens K, Meijer AB, van den Biggelaar M, (2018) "Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30153514 30153514]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.08.011 10.1016/j.jprot.2018.08.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30153514 33]. | ||
+ | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
+ | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. |
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 October 14, 2018.