Line 27: | Line 27: | ||
==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 Feb. | + | 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 Feb. 11, 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: [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 856: | Line 856: | ||
#Shalit T, Elinger D, Savidor A, Gabashvili A, Levin Y, (2015) "MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer." <i>J Proteome Res</i> <b>14</b>(4):1979–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25780947 25780947]; doi: [https://dx.doi.org/10.1021/pr501045t 10.1021/pr501045t]; GPMDB: [http://gpmdb.org/data/keyword/25780947 12]. | #Shalit T, Elinger D, Savidor A, Gabashvili A, Levin Y, (2015) "MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer." <i>J Proteome Res</i> <b>14</b>(4):1979–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25780947 25780947]; doi: [https://dx.doi.org/10.1021/pr501045t 10.1021/pr501045t]; GPMDB: [http://gpmdb.org/data/keyword/25780947 12]. | ||
#Markmann S, Thelen M, Cornils K, Schweizer M, Brocke-Ahmadinejad N, Willnow T, Heeren J, Gieselmann V, Braulke T, Kollmann K, (2015) "Lrp1/LDL Receptor Play Critical Roles in Mannose 6-Phosphate-Independent Lysosomal Enzyme Targeting." <i>Traffic</i> <b>16</b>(7):743–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25786328 25786328]; doi: [https://dx.doi.org/10.1111/tra.12284 10.1111/tra.12284]; GPMDB: [http://gpmdb.org/data/keyword/25786328 3]. | #Markmann S, Thelen M, Cornils K, Schweizer M, Brocke-Ahmadinejad N, Willnow T, Heeren J, Gieselmann V, Braulke T, Kollmann K, (2015) "Lrp1/LDL Receptor Play Critical Roles in Mannose 6-Phosphate-Independent Lysosomal Enzyme Targeting." <i>Traffic</i> <b>16</b>(7):743–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25786328 25786328]; doi: [https://dx.doi.org/10.1111/tra.12284 10.1111/tra.12284]; GPMDB: [http://gpmdb.org/data/keyword/25786328 3]. | ||
- | #Manousopoulou A, Woo J, Woelk CH, Johnston HE, Singhania A, Hawkes C, Garbis SD, Carare RO, (2015) "Are you also what your mother eats? Distinct proteomic portrait as a result of maternal high-fat diet in the cerebral cortex of the adult mouse." <i>Int J Obes (Lond)</i> <b>39</b>(8):1325–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25797609 25797609]; doi: [https://dx.doi.org/10.1038/ijo.2015.35 10.1038/ijo.2015.35]; GPMDB: [http://gpmdb.org/data/keyword/25797609 | + | #Manousopoulou A, Woo J, Woelk CH, Johnston HE, Singhania A, Hawkes C, Garbis SD, Carare RO, (2015) "Are you also what your mother eats? Distinct proteomic portrait as a result of maternal high-fat diet in the cerebral cortex of the adult mouse." <i>Int J Obes (Lond)</i> <b>39</b>(8):1325–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25797609 25797609]; doi: [https://dx.doi.org/10.1038/ijo.2015.35 10.1038/ijo.2015.35]; GPMDB: [http://gpmdb.org/data/keyword/25797609 61]. |
#Bracht T, Schweinsberg V, Trippler M, Kohl M, Ahrens M, Padden J, Naboulsi W, Barkovits K, Megger DA, Eisenacher M, Borchers CH, Schlaak JF, Hoffmann AC, Weber F, Baba HA, Meyer HE, Sitek B, (2015) "Analysis of disease-associated protein expression using quantitative proteomics—fibulin-5 is expressed in association with hepatic fibrosis." <i>J Proteome Res</i> <b>14</b>(5):2278–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25807371 25807371]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00053 10.1021/acs.jproteome.5b00053]; GPMDB: [http://gpmdb.org/data/keyword/25807371 27]. | #Bracht T, Schweinsberg V, Trippler M, Kohl M, Ahrens M, Padden J, Naboulsi W, Barkovits K, Megger DA, Eisenacher M, Borchers CH, Schlaak JF, Hoffmann AC, Weber F, Baba HA, Meyer HE, Sitek B, (2015) "Analysis of disease-associated protein expression using quantitative proteomics—fibulin-5 is expressed in association with hepatic fibrosis." <i>J Proteome Res</i> <b>14</b>(5):2278–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25807371 25807371]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00053 10.1021/acs.jproteome.5b00053]; GPMDB: [http://gpmdb.org/data/keyword/25807371 27]. | ||
#Broncel M, Serwa RA, Ciepla P, Krause E, Dallman MJ, Magee AI, Tate EW, (2015) "Multifunctional reagents for quantitative proteome-wide analysis of protein modification in human cells and dynamic profiling of protein lipidation during vertebrate development." <i>Angew Chem Int Ed Engl</i> <b>54</b>(20):5948–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25807930 25807930]; doi: [https://dx.doi.org/10.1002/anie.201500342 10.1002/anie.201500342]; GPMDB: [http://gpmdb.org/data/keyword/25807930 1]. | #Broncel M, Serwa RA, Ciepla P, Krause E, Dallman MJ, Magee AI, Tate EW, (2015) "Multifunctional reagents for quantitative proteome-wide analysis of protein modification in human cells and dynamic profiling of protein lipidation during vertebrate development." <i>Angew Chem Int Ed Engl</i> <b>54</b>(20):5948–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25807930 25807930]; doi: [https://dx.doi.org/10.1002/anie.201500342 10.1002/anie.201500342]; GPMDB: [http://gpmdb.org/data/keyword/25807930 1]. | ||
Line 1,764: | Line 1,764: | ||
#Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, Thomson T, (2018) "Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons." <i>Cell</i> <b>172</b>(1-2):262–274.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29328915 29328915]; doi: [https://dx.doi.org/10.1016/j.cell.2017.12.022 10.1016/j.cell.2017.12.022]; GPMDB: [http://gpmdb.org/data/keyword/29328915 6]. | #Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, Thomson T, (2018) "Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons." <i>Cell</i> <b>172</b>(1-2):262–274.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29328915 29328915]; doi: [https://dx.doi.org/10.1016/j.cell.2017.12.022 10.1016/j.cell.2017.12.022]; GPMDB: [http://gpmdb.org/data/keyword/29328915 6]. | ||
#Khan SY, Ali M, Kabir F, Renuse S, Na CH, Talbot CC Jr, Hackett SF, Riazuddin SA, (2018) "Proteome Profiling of Developing Murine Lens Through Mass Spectrometry." <i>Invest Ophthalmol Vis Sci</i> <b>59</b>(1):100–107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29332127 29332127]; doi: [https://dx.doi.org/10.1167/iovs.17-21601 10.1167/iovs.17-21601]; GPMDB: [http://gpmdb.org/data/keyword/29332127 3]. | #Khan SY, Ali M, Kabir F, Renuse S, Na CH, Talbot CC Jr, Hackett SF, Riazuddin SA, (2018) "Proteome Profiling of Developing Murine Lens Through Mass Spectrometry." <i>Invest Ophthalmol Vis Sci</i> <b>59</b>(1):100–107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29332127 29332127]; doi: [https://dx.doi.org/10.1167/iovs.17-21601 10.1167/iovs.17-21601]; GPMDB: [http://gpmdb.org/data/keyword/29332127 3]. | ||
- | #Kim DK, Park J, Han D, Yang J, Kim A, Woo J, Kim Y, Mook-Jung I, (2018) "Molecular and functional signatures in a novel Alzheimer's disease mouse model assessed by quantitative proteomics." <i>Mol Neurodegener</i> <b>13</b>(1):2; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29338754 29338754]; doi: [https://dx.doi.org/10.1186/s13024-017-0234-4 10.1186/s13024-017-0234-4]; GPMDB: [http://gpmdb.org/data/keyword/29338754 | + | #Kim DK, Park J, Han D, Yang J, Kim A, Woo J, Kim Y, Mook-Jung I, (2018) "Molecular and functional signatures in a novel Alzheimer's disease mouse model assessed by quantitative proteomics." <i>Mol Neurodegener</i> <b>13</b>(1):2; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29338754 29338754]; doi: [https://dx.doi.org/10.1186/s13024-017-0234-4 10.1186/s13024-017-0234-4]; GPMDB: [http://gpmdb.org/data/keyword/29338754 8]. |
#Sousa DZ, Visser M, van Gelder AH, Boeren S, Pieterse MM, Pinkse MWH, Verhaert PDEM, Vogt C, Franke S, Kümmel S, Stams AJM, (2018) "The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways." <i>Nat Commun</i> <b>9</b>(1):239; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29339722 29339722]; doi: [https://dx.doi.org/10.1038/s41467-017-02518-9 10.1038/s41467-017-02518-9]; GPMDB: [http://gpmdb.org/data/keyword/29339722 84]. | #Sousa DZ, Visser M, van Gelder AH, Boeren S, Pieterse MM, Pinkse MWH, Verhaert PDEM, Vogt C, Franke S, Kümmel S, Stams AJM, (2018) "The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways." <i>Nat Commun</i> <b>9</b>(1):239; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29339722 29339722]; doi: [https://dx.doi.org/10.1038/s41467-017-02518-9 10.1038/s41467-017-02518-9]; GPMDB: [http://gpmdb.org/data/keyword/29339722 84]. | ||
#Vranka JA, Staverosky JA, Reddy AP, Wilmarth PA, David LL, Acott TS, Russell P, Raghunathan VK, (2018) "Biomechanical Rigidity and Quantitative Proteomics Analysis of Segmental Regions of the Trabecular Meshwork at Physiologic and Elevated Pressures." <i>Invest Ophthalmol Vis Sci</i> <b>59</b>(1):246–259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29340639 29340639]; doi: [https://dx.doi.org/10.1167/iovs.17-22759 10.1167/iovs.17-22759]; GPMDB: [http://gpmdb.org/data/keyword/29340639 2]. | #Vranka JA, Staverosky JA, Reddy AP, Wilmarth PA, David LL, Acott TS, Russell P, Raghunathan VK, (2018) "Biomechanical Rigidity and Quantitative Proteomics Analysis of Segmental Regions of the Trabecular Meshwork at Physiologic and Elevated Pressures." <i>Invest Ophthalmol Vis Sci</i> <b>59</b>(1):246–259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29340639 29340639]; doi: [https://dx.doi.org/10.1167/iovs.17-22759 10.1167/iovs.17-22759]; GPMDB: [http://gpmdb.org/data/keyword/29340639 2]. | ||
+ | #Drabikowski K, Ferralli J, Kistowski M, Oledzki J, Dadlez M, Chiquet-Ehrismann R, (2018) "Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling." <i>Sci Rep</i> <b>8</b>(1):1139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348603 29348603]; doi: [https://dx.doi.org/10.1038/s41598-018-19424-9 10.1038/s41598-018-19424-9]; GPMDB: [http://gpmdb.org/data/keyword/29348603 37]. | ||
#Gao Y, Ge W, (2018) "The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis." <i>Cell Death Dis</i> <b>9</b>(2):33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348610 29348610]; doi: [https://dx.doi.org/10.1038/s41419-017-0040-5 10.1038/s41419-017-0040-5]; GPMDB: [http://gpmdb.org/data/keyword/29348610 2]. | #Gao Y, Ge W, (2018) "The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis." <i>Cell Death Dis</i> <b>9</b>(2):33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348610 29348610]; doi: [https://dx.doi.org/10.1038/s41419-017-0040-5 10.1038/s41419-017-0040-5]; GPMDB: [http://gpmdb.org/data/keyword/29348610 2]. | ||
#Mustafa DAM, Pedrosa RMSM, Smid M, van der Weiden M, de Weerd V, Nigg AL, Berrevoets C, Zeneyedpour L, Priego N, Valiente M, Luider TM, Debets R, Martens JWM, Foekens JA, Sieuwerts AM, Kros JM, (2018) "T lymphocytes facilitate brain metastasis of breast cancer by inducing Guanylate-Binding Protein 1 expression." <i>Acta Neuropathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350274 29350274]; doi: [https://dx.doi.org/10.1007/s00401-018-1806-2 10.1007/s00401-018-1806-2]; GPMDB: [http://gpmdb.org/data/keyword/29350274 6]. | #Mustafa DAM, Pedrosa RMSM, Smid M, van der Weiden M, de Weerd V, Nigg AL, Berrevoets C, Zeneyedpour L, Priego N, Valiente M, Luider TM, Debets R, Martens JWM, Foekens JA, Sieuwerts AM, Kros JM, (2018) "T lymphocytes facilitate brain metastasis of breast cancer by inducing Guanylate-Binding Protein 1 expression." <i>Acta Neuropathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350274 29350274]; doi: [https://dx.doi.org/10.1007/s00401-018-1806-2 10.1007/s00401-018-1806-2]; GPMDB: [http://gpmdb.org/data/keyword/29350274 6]. | ||
Line 1,773: | Line 1,774: | ||
#Topf U, Suppanz I, Samluk L, Wrobel L, Böser A, Sakowska P, Knapp B, Pietrzyk MK, Chacinska A, Warscheid B, (2018) "Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species." <i>Nat Commun</i> <b>9</b>(1):324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29358734 29358734]; doi: [https://dx.doi.org/10.1038/s41467-017-02694-8 10.1038/s41467-017-02694-8]; GPMDB: [http://gpmdb.org/data/keyword/29358734 96]. | #Topf U, Suppanz I, Samluk L, Wrobel L, Böser A, Sakowska P, Knapp B, Pietrzyk MK, Chacinska A, Warscheid B, (2018) "Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species." <i>Nat Commun</i> <b>9</b>(1):324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29358734 29358734]; doi: [https://dx.doi.org/10.1038/s41467-017-02694-8 10.1038/s41467-017-02694-8]; GPMDB: [http://gpmdb.org/data/keyword/29358734 96]. | ||
#Johnston HE, Carter MJ, Larrayoz M, Clarke J, Garbis SD, Oscier D, Strefford JC, Steele AJ, Walewska R, Cragg MS, (2018) "Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29367434 29367434]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000539 10.1074/mcp.RA117.000539]; GPMDB: [http://gpmdb.org/data/keyword/29367434 2]. | #Johnston HE, Carter MJ, Larrayoz M, Clarke J, Garbis SD, Oscier D, Strefford JC, Steele AJ, Walewska R, Cragg MS, (2018) "Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29367434 29367434]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000539 10.1074/mcp.RA117.000539]; GPMDB: [http://gpmdb.org/data/keyword/29367434 2]. | ||
+ | #Kostas M, Haugsten EM, Zhen Y, Sorensen V, Szybowska P, Fiorito E, Lorenz S, de Souza GA, Wiedlocha A, Wesche J, (2018) "The phosphatase PTPRG controls FGFR1 activity and influences sensitivity to FGFR kinase inhibitors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29371290 29371290]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000538 10.1074/mcp.RA117.000538]; GPMDB: [http://gpmdb.org/data/keyword/29371290 54]. | ||
+ | #Adav SS, Subbaiaih RS, Kerk SK, Lee AY, Lai HY, Ng KW, Sze SK, Schmidtchen A, (2018) "Studies on the Proteome of Human Hair - Identification of Histones and Deamidated Keratins." <i>Sci Rep</i> <b>8</b>(1):1599; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29371649 29371649]; doi: [https://dx.doi.org/10.1038/s41598-018-20041-9 10.1038/s41598-018-20041-9]; GPMDB: [http://gpmdb.org/data/keyword/29371649 18]. | ||
+ | #Zhou Y, Gao J, Zhu H, Xu J, He H, Gu L, Wang H, Chen J, Ma D, Zhou H, Zheng J, (2018) "Enhancing Membrane Protein Identification Using a Simplified Centrifugation and Detergent-Based Membrane Extraction Approach." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29376338 29376338]; doi: [https://dx.doi.org/10.1021/acs.analchem.7b03710 10.1021/acs.analchem.7b03710]; GPMDB: [http://gpmdb.org/data/keyword/29376338 24]. |
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 Feb. 11, 2018.