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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 Mar. 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]. | ||
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#Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | #Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | ||
#Beckley JR, Chen JS, Yang Y, Peng J, Gould KL, (2015) "A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival." <i>Mol Cell Proteomics</i> <b>14</b>(12):3132–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412298 26412298]; doi: [https://dx.doi.org/10.1074/mcp.M115.050039 10.1074/mcp.M115.050039]; GPMDB: [http://gpmdb.org/data/keyword/26412298 246]. | #Beckley JR, Chen JS, Yang Y, Peng J, Gould KL, (2015) "A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival." <i>Mol Cell Proteomics</i> <b>14</b>(12):3132–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412298 26412298]; doi: [https://dx.doi.org/10.1074/mcp.M115.050039 10.1074/mcp.M115.050039]; GPMDB: [http://gpmdb.org/data/keyword/26412298 246]. | ||
- | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 | + | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 934]. |
#Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | #Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | ||
#Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | #Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | ||
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#Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [http://gpmdb.org/data/keyword/29145436 57]. | #Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [http://gpmdb.org/data/keyword/29145436 57]. | ||
#Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [http://gpmdb.org/data/keyword/29145658 4]. | #Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [http://gpmdb.org/data/keyword/29145658 4]. | ||
+ | #Le Guerroué F, Eck F, Jung J, Starzetz T, Mittelbronn M, Kaulich M, Behrends C, (2017) "Autophagosomal Content Profiling Reveals an LC3C-Dependent Piecemeal Mitophagy Pathway." <i>Mol Cell</i> <b>68</b>(4):786–796.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29149599 29149599]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.10.029 10.1016/j.molcel.2017.10.029]; GPMDB: [http://gpmdb.org/data/keyword/29149599 138]. | ||
#Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS, (2017) "Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29155090 29155090]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.008 10.1016/j.jprot.2017.11.008]; GPMDB: [http://gpmdb.org/data/keyword/29155090 21]. | #Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS, (2017) "Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29155090 29155090]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.008 10.1016/j.jprot.2017.11.008]; GPMDB: [http://gpmdb.org/data/keyword/29155090 21]. | ||
#Föll MC, Fahrner M, Gretzmeier C, Thoma K, Biniossek ML, Kiritsi D, Meiss F, Schilling O, Nyström A, Kern JS, (2017) "Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas." <i>Matrix Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29158163 29158163]; doi: [https://dx.doi.org/10.1016/j.matbio.2017.11.004 10.1016/j.matbio.2017.11.004]; GPMDB: [http://gpmdb.org/data/keyword/29158163 24]. | #Föll MC, Fahrner M, Gretzmeier C, Thoma K, Biniossek ML, Kiritsi D, Meiss F, Schilling O, Nyström A, Kern JS, (2017) "Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas." <i>Matrix Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29158163 29158163]; doi: [https://dx.doi.org/10.1016/j.matbio.2017.11.004 10.1016/j.matbio.2017.11.004]; GPMDB: [http://gpmdb.org/data/keyword/29158163 24]. | ||
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#Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [http://gpmdb.org/data/keyword/29281840 2]. | #Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [http://gpmdb.org/data/keyword/29281840 2]. | ||
#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]. | ||
+ | #Kelley RC, McDonagh B, Ferreira LF, (2018) "Advanced aging causes diaphragm functional abnormalities, global proteome remodeling, and loss of mitochondrial cysteine redox flexibility in mice." <i>Exp Gerontol</i> <b>103</b>:69–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29289553 29289553]; doi: [https://dx.doi.org/10.1016/j.exger.2017.12.017 10.1016/j.exger.2017.12.017]; GPMDB: [http://gpmdb.org/data/keyword/29289553 24]. | ||
#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]. | #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]. | ||
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#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]. | #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]. | ||
+ | #Walheim E, Wiśniewski JR, Jastroch M, (2018) "Respiromics - An integrative analysis linking mitochondrial bioenergetics to molecular signatures." <i>Mol Metab</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29361498 29361498]; doi: [https://dx.doi.org/10.1016/j.molmet.2018.01.002 10.1016/j.molmet.2018.01.002]; GPMDB: [http://gpmdb.org/data/keyword/29361498 32]. | ||
#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]. | #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]. | ||
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#Grossegesse M, Doellinger J, Fritsch A, Laue M, Piesker J, Schaade L, Nitsche A, (2018) "Global ubiquitination analysis reveals extensive modification and proteasomal degradation of cowpox virus proteins, but preservation of viral cores." <i>Sci Rep</i> <b>8</b>(1):1807; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29379051 29379051]; doi: [https://dx.doi.org/10.1038/s41598-018-20130-9 10.1038/s41598-018-20130-9]; GPMDB: [http://gpmdb.org/data/keyword/29379051 16]. | #Grossegesse M, Doellinger J, Fritsch A, Laue M, Piesker J, Schaade L, Nitsche A, (2018) "Global ubiquitination analysis reveals extensive modification and proteasomal degradation of cowpox virus proteins, but preservation of viral cores." <i>Sci Rep</i> <b>8</b>(1):1807; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29379051 29379051]; doi: [https://dx.doi.org/10.1038/s41598-018-20130-9 10.1038/s41598-018-20130-9]; GPMDB: [http://gpmdb.org/data/keyword/29379051 16]. | ||
#Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER, (2018) "The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29386236 29386236]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000596 10.1074/mcp.RA118.000596]; GPMDB: [http://gpmdb.org/data/keyword/29386236 12]. | #Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER, (2018) "The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29386236 29386236]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000596 10.1074/mcp.RA118.000596]; GPMDB: [http://gpmdb.org/data/keyword/29386236 12]. | ||
+ | #Schanzenbächer CT, Langer JD, Schuman EM, (2018) "Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29447110 29447110]; doi: [https://dx.doi.org/10.7554/eLife.33322 10.7554/eLife.33322]; GPMDB: [http://gpmdb.org/data/keyword/29447110 78]. | ||
+ | #Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L, (2018) "Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29451788 29451788]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00788 10.1021/acs.jproteome.7b00788]; GPMDB: [http://gpmdb.org/data/keyword/29451788 36]. | ||
+ | #Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M, (2018) "Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453283 29453283]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001484 10.1074/jbc.RA117.001484]; GPMDB: [http://gpmdb.org/data/keyword/29453283 39]. | ||
+ | #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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/29467492 6]. | ||
+ | #Zhan Y, Marchand CH, Maes A, Mauries A, Sun Y, Dhaliwal JS, Uniacke J, Arragain S, Jiang H, Gold ND, Martin VJJ, Lemaire SD, Zerges W, (2018) "Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii." <i>PLoS One</i> <b>13</b>(2):e0185039; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29481573 29481573]; doi: [https://dx.doi.org/10.1371/journal.pone.0185039 10.1371/journal.pone.0185039]; GPMDB: [http://gpmdb.org/data/keyword/29481573 16]. | ||
+ | #Zeiner PS, Zinke J, Kowalewski DJ, Bernatz S, Tichy J, Ronellenfitsch MW, Thorsen F, Berger A, Forster MT, Muller A, Steinbach JP, Beschorner R, Wischhusen J, Kvasnicka HM, Plate KH, Stefanović S, Weide B, Mittelbronn M, Harter PN, (2018) "CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival." <i>Acta Neuropathol Commun</i> <b>6</b>(1):18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29490700 29490700]; doi: [https://dx.doi.org/10.1186/s40478-018-0521-5 10.1186/s40478-018-0521-5]; GPMDB: [http://gpmdb.org/data/keyword/29490700 20]. | ||
+ | #Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE, (2018) "Phosphoproteomics analysis identifies novel candidate substrates of the non-receptor tyrosine kinase, SRMS." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29496907 29496907]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000643 10.1074/mcp.RA118.000643]; GPMDB: [http://gpmdb.org/data/keyword/29496907 4]. | ||
+ | #Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, Yuan J, Chen R, Li Y, Ge Z, Ji J, Zhang L, Wang J, Li Z, Lai Y, Hu Y, Li Y, Li Y, Gao J, Chen L, Xu J, Zhang C, Jung SY, Choi JM, Jain A, Liu M, Song L, Liu W, Guo G, Gong T, Huang Y, Qiu Y, Huang W, Shi T, Zhu W, Wang Y, He F, Shen L, Qin J, (2018) "A proteomic landscape of diffuse-type gastric cancer." <i>Nat Commun</i> <b>9</b>(1):1012; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520031 29520031]; doi: [https://dx.doi.org/10.1038/s41467-018-03121-2 10.1038/s41467-018-03121-2]; GPMDB: [http://gpmdb.org/data/keyword/29520031 55]. |
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 Mar. 11, 2018.