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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 Feb. 3, 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]. | ||
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#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 49]. | ||
#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]. | ||
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#Abdelmegid S, Murugaiyan J, Abo-Ismail M, Caswell JL, Kelton D, Kirby GM, (2017) "Identification of Host Defense-Related Proteins Using Label-Free Quantitative Proteomic Analysis of Milk Whey from Cows with Staphylococcus aureus Subclinical Mastitis." <i>Int J Mol Sci</i> <b>19</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29283389 29283389]; doi: [https://dx.doi.org/10.3390/ijms19010078 10.3390/ijms19010078]; GPMDB: [http://gpmdb.org/data/keyword/29283389 11]. | #Abdelmegid S, Murugaiyan J, Abo-Ismail M, Caswell JL, Kelton D, Kirby GM, (2017) "Identification of Host Defense-Related Proteins Using Label-Free Quantitative Proteomic Analysis of Milk Whey from Cows with Staphylococcus aureus Subclinical Mastitis." <i>Int J Mol Sci</i> <b>19</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29283389 29283389]; doi: [https://dx.doi.org/10.3390/ijms19010078 10.3390/ijms19010078]; GPMDB: [http://gpmdb.org/data/keyword/29283389 11]. | ||
#Ritz D, Sani E, Debiec H, Ronco P, Neri D, Fugmann T, (2018) "Membranal and blood-soluble HLA class II peptidome analyses using data-dependent and independent acquisition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29314611 29314611]; doi: [https://dx.doi.org/10.1002/pmic.201700246 10.1002/pmic.201700246]; GPMDB: [http://gpmdb.org/data/keyword/29314611 27]. | #Ritz D, Sani E, Debiec H, Ronco P, Neri D, Fugmann T, (2018) "Membranal and blood-soluble HLA class II peptidome analyses using data-dependent and independent acquisition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29314611 29314611]; doi: [https://dx.doi.org/10.1002/pmic.201700246 10.1002/pmic.201700246]; GPMDB: [http://gpmdb.org/data/keyword/29314611 27]. | ||
+ | #Grube L, Dellen R, Kruse F, Schwender H, Stühler K, Poschmann G, (2018) "Mining the Secretome of C2C12 Muscle Cells: Data Dependent Experimental Approach To Analyze Protein Secretion Using Label-Free Quantification and Peptide Based Analysis." <i>J Proteome Res</i> <b>17</b>(2):879–890; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29322779 29322779]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00684 10.1021/acs.jproteome.7b00684]; GPMDB: [http://gpmdb.org/data/keyword/29322779 20]. | ||
#Nassa G, Giurato G, Cimmino G, Rizzo F, Ravo M, Salvati A, Nyman TA, Zhu Y, Vesterlund M, Lehtiö J, Golino P, Weisz A, Tarallo R, (2018) "Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications." <i>Sci Rep</i> <b>8</b>(1):498; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29323256 29323256]; doi: [https://dx.doi.org/10.1038/s41598-017-18985-5 10.1038/s41598-017-18985-5]; GPMDB: [http://gpmdb.org/data/keyword/29323256 1]. | #Nassa G, Giurato G, Cimmino G, Rizzo F, Ravo M, Salvati A, Nyman TA, Zhu Y, Vesterlund M, Lehtiö J, Golino P, Weisz A, Tarallo R, (2018) "Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications." <i>Sci Rep</i> <b>8</b>(1):498; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29323256 29323256]; doi: [https://dx.doi.org/10.1038/s41598-017-18985-5 10.1038/s41598-017-18985-5]; GPMDB: [http://gpmdb.org/data/keyword/29323256 1]. | ||
#Thriene K, Grüning BA, Bornert O, Erxleben A, Leppert J, Athanasiou I, Weber E, Kiritsi D, Nyström A, Reinheckel T, Backofen R, Has C, Bruckner-Tuderman L, Dengjel J, (2018) "Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29326176 29326176]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000437 10.1074/mcp.RA117.000437]; GPMDB: [http://gpmdb.org/data/keyword/29326176 14]. | #Thriene K, Grüning BA, Bornert O, Erxleben A, Leppert J, Athanasiou I, Weber E, Kiritsi D, Nyström A, Reinheckel T, Backofen R, Has C, Bruckner-Tuderman L, Dengjel J, (2018) "Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29326176 29326176]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000437 10.1074/mcp.RA117.000437]; GPMDB: [http://gpmdb.org/data/keyword/29326176 14]. | ||
+ | #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 4]. | ||
+ | #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]. | ||
- | #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 1]. | + | #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]. | ||
+ | #Schönke M, Björnholm M, Chibalin AV, Zierath JR, Deshmukh AS, (2018) "Proteomics Analysis of Skeletal Muscle from Leptin-Deficient Ob/Ob Mice Reveals Adaptive Remodeling of Metabolic Characteristics and Fiber Type Composition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350465 29350465]; doi: [https://dx.doi.org/10.1002/pmic.201700375 10.1002/pmic.201700375]; GPMDB: [http://gpmdb.org/data/keyword/29350465 22]. | ||
+ | #Ongay S, Langelaar-Makkinje M, Stoop MP, Liu N, Overkleeft H, Luider TM, Groothuis GMM, Bischoff R, (2018) "Cleavable crosslinkers as tissue fixation reagents for proteomic analysis." <i>Chembiochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29356267 29356267]; doi: [https://dx.doi.org/10.1002/cbic.201700625 10.1002/cbic.201700625]; GPMDB: [http://gpmdb.org/data/keyword/29356267 15]. | ||
#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]. |
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. 3, 2018.