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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 December 16, 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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#Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P, (2017) "eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs." <i>Nucleic Acids Res</i> <b>45</b>(13):7997–8013; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28541577 28541577]; doi: [https://dx.doi.org/10.1093/nar/gkx469 10.1093/nar/gkx469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28541577 19]. | #Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P, (2017) "eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs." <i>Nucleic Acids Res</i> <b>45</b>(13):7997–8013; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28541577 28541577]; doi: [https://dx.doi.org/10.1093/nar/gkx469 10.1093/nar/gkx469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28541577 19]. | ||
#Hakimi O, Ternette N, Murphy R, Kessler BM, Carr A, (2017) "A quantitative label-free analysis of the extracellular proteome of human supraspinatus tendon reveals damage to the pericellular and elastic fibre niches in torn and aged tissue." <i>PLoS One</i> <b>12</b>(5):e0177656; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28542244 28542244]; doi: [https://dx.doi.org/10.1371/journal.pone.0177656 10.1371/journal.pone.0177656]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28542244 116]. | #Hakimi O, Ternette N, Murphy R, Kessler BM, Carr A, (2017) "A quantitative label-free analysis of the extracellular proteome of human supraspinatus tendon reveals damage to the pericellular and elastic fibre niches in torn and aged tissue." <i>PLoS One</i> <b>12</b>(5):e0177656; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28542244 28542244]; doi: [https://dx.doi.org/10.1371/journal.pone.0177656 10.1371/journal.pone.0177656]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28542244 116]. | ||
+ | #Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke DM, Parker GJ, Rice RH, (2017) "Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides." <i>Proteomics</i> <b>17</b>(13-14):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28544375 28544375]; doi: [https://dx.doi.org/10.1002/pmic.201600462 10.1002/pmic.201600462]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28544375 24]. | ||
#Kume K, Cantwell H, Neumann FR, Jones AW, Snijders AP, Nurse P, (2017) "A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control." <i>PLoS Genet</i> <b>13</b>(5):e1006767; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28545058 28545058]; doi: [https://dx.doi.org/10.1371/journal.pgen.1006767 10.1371/journal.pgen.1006767]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28545058 192]. | #Kume K, Cantwell H, Neumann FR, Jones AW, Snijders AP, Nurse P, (2017) "A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control." <i>PLoS Genet</i> <b>13</b>(5):e1006767; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28545058 28545058]; doi: [https://dx.doi.org/10.1371/journal.pgen.1006767 10.1371/journal.pgen.1006767]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28545058 192]. | ||
#Meier SM, Kreutz D, Winter L, Klose MHM, Cseh K, Weiss T, Bileck A, Alte B, Mader JC, Jana S, Chatterjee A, Bhattacharyya A, Hejl M, Jakupec MA, Heffeter P, Berger W, Hartinger CG, Keppler BK, Wiche G, Gerner C, (2017) "An Organoruthenium Anticancer Agent Shows Unexpected Target Selectivity For Plectin." <i>Angew Chem Int Ed Engl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28547791 28547791]; doi: [https://dx.doi.org/10.1002/anie.201702242 10.1002/anie.201702242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28547791 4]. | #Meier SM, Kreutz D, Winter L, Klose MHM, Cseh K, Weiss T, Bileck A, Alte B, Mader JC, Jana S, Chatterjee A, Bhattacharyya A, Hejl M, Jakupec MA, Heffeter P, Berger W, Hartinger CG, Keppler BK, Wiche G, Gerner C, (2017) "An Organoruthenium Anticancer Agent Shows Unexpected Target Selectivity For Plectin." <i>Angew Chem Int Ed Engl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28547791 28547791]; doi: [https://dx.doi.org/10.1002/anie.201702242 10.1002/anie.201702242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28547791 4]. | ||
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#Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Özturk VÖ, Afacan B, Emingil G, Belibasakis GN, (2018) "Targeted proteomics guided by label-free global proteome analysis in saliva reveal transition signatures from health to periodontal disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29610270 29610270]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000718 10.1074/mcp.RA118.000718]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29610270 54]. | #Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Özturk VÖ, Afacan B, Emingil G, Belibasakis GN, (2018) "Targeted proteomics guided by label-free global proteome analysis in saliva reveal transition signatures from health to periodontal disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29610270 29610270]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000718 10.1074/mcp.RA118.000718]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29610270 54]. | ||
#Sipilä KH, Drushinin K, Rappu P, Jokinen J, Salminen TA, Salo AM, Käpylä J, Myllyharju J, Heino J, (2018) "Proline hydroxylation in collagen supports integrin binding by two distinct mechanisms." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29615493 29615493]; doi: [https://dx.doi.org/10.1074/jbc.RA118.002200 10.1074/jbc.RA118.002200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29615493 54]. | #Sipilä KH, Drushinin K, Rappu P, Jokinen J, Salminen TA, Salo AM, Käpylä J, Myllyharju J, Heino J, (2018) "Proline hydroxylation in collagen supports integrin binding by two distinct mechanisms." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29615493 29615493]; doi: [https://dx.doi.org/10.1074/jbc.RA118.002200 10.1074/jbc.RA118.002200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29615493 54]. | ||
+ | #Lobas AA, Pyatnitskiy MA, Chernobrovkin AL, Ilina IY, Karpov DS, Solovyeva EM, Kuznetsova KG, Ivanov MV, Lyssuk EY, Kliuchnikova AA, Voronko OE, Larin SS, Zubarev RA, Gorshkov MV, Moshkovskii SA, (2018) "Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics." <i>J Proteome Res</i> <b>17</b>(5):1801–1811; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29619825 29619825]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00841 10.1021/acs.jproteome.7b00841]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29619825 48]. | ||
#Lim S, Kim D, Ju S, Shin S, Cho IJ, Park SH, Grailhe R, Lee C, Kim YK, (2018) "Glioblastoma-secreted soluble CD44 activates tau pathology in the brain." <i>Exp Mol Med</i> <b>50</b>(4):5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29622771 29622771]; doi: [https://dx.doi.org/10.1038/s12276-017-0008-7 10.1038/s12276-017-0008-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29622771 2]. | #Lim S, Kim D, Ju S, Shin S, Cho IJ, Park SH, Grailhe R, Lee C, Kim YK, (2018) "Glioblastoma-secreted soluble CD44 activates tau pathology in the brain." <i>Exp Mol Med</i> <b>50</b>(4):5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29622771 29622771]; doi: [https://dx.doi.org/10.1038/s12276-017-0008-7 10.1038/s12276-017-0008-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29622771 2]. | ||
#Sanz-Bravo A, Alvarez-Navarro C, Martín-Esteban A, Barnea E, Admon A, López de Castro JA, (2018) "Ranking the contribution of ankylosing spondylitis-associated ERAP1 polymorphisms to shaping the HLA-B*27 peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29632046 29632046]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000565 10.1074/mcp.RA117.000565]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29632046 15]. | #Sanz-Bravo A, Alvarez-Navarro C, Martín-Esteban A, Barnea E, Admon A, López de Castro JA, (2018) "Ranking the contribution of ankylosing spondylitis-associated ERAP1 polymorphisms to shaping the HLA-B*27 peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29632046 29632046]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000565 10.1074/mcp.RA117.000565]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29632046 15]. | ||
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#Mao F, Lei J, Enoch O, Wei M, Zhao C, Quan Y, Yu W, (2018) "Quantitative proteomics of Bombyx mori after BmNPV challenge." <i>J Proteomics</i> <b>181</b>:142–151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29674014 29674014]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.04.010 10.1016/j.jprot.2018.04.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29674014 18]. | #Mao F, Lei J, Enoch O, Wei M, Zhao C, Quan Y, Yu W, (2018) "Quantitative proteomics of Bombyx mori after BmNPV challenge." <i>J Proteomics</i> <b>181</b>:142–151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29674014 29674014]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.04.010 10.1016/j.jprot.2018.04.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29674014 18]. | ||
#Johnston D, Malo Estepa I, Ebhardt HA, Crowe MA, Diskin MG, (2018) "Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle." <i>Theriogenology</i> <b>114</b>:301–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29677633 29677633]; doi: [https://dx.doi.org/10.1016/j.theriogenology.2018.04.008 10.1016/j.theriogenology.2018.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29677633 63]. | #Johnston D, Malo Estepa I, Ebhardt HA, Crowe MA, Diskin MG, (2018) "Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle." <i>Theriogenology</i> <b>114</b>:301–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29677633 29677633]; doi: [https://dx.doi.org/10.1016/j.theriogenology.2018.04.008 10.1016/j.theriogenology.2018.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29677633 63]. | ||
+ | #Zhang X, Chang H, Dong Z, Zhang Y, Zhao D, Ye L, Xia Q, Zhao P, (2018) "Comparative Proteome Analysis Reveals that Cuticular Proteins Analogous to Peritrophin-Motif Proteins are Involved in the Regeneration of Chitin Layer in the Silk Gland of Bombyx mori at the Molting Stage." <i>Proteomics</i> <b>18</b>(19):e1700389; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29687606 29687606]; doi: [https://dx.doi.org/10.1002/pmic.201700389 10.1002/pmic.201700389]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29687606 6]. | ||
#Komov L, Kadosh DM, Barnea E, Milner E, Hendler A, Admon A, (2018) "Cell Surface MHC Class I Expression is Limited by the Availability of Peptide-Receptive 'Empty' Molecules Rather than by the Supply of Peptide Ligands." <i>Proteomics</i> <b></b>:e1700248; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707912 29707912]; doi: [https://dx.doi.org/10.1002/pmic.201700248 10.1002/pmic.201700248]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707912 35]. | #Komov L, Kadosh DM, Barnea E, Milner E, Hendler A, Admon A, (2018) "Cell Surface MHC Class I Expression is Limited by the Availability of Peptide-Receptive 'Empty' Molecules Rather than by the Supply of Peptide Ligands." <i>Proteomics</i> <b></b>:e1700248; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707912 29707912]; doi: [https://dx.doi.org/10.1002/pmic.201700248 10.1002/pmic.201700248]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707912 35]. | ||
#Rosting C, Yu J, Cooper HJ, (2018) "High Field Asymmetric Waveform Ion Mobility Spectrometry in Nontargeted Bottom-up Proteomics of Dried Blood Spots." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707944 29707944]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00746 10.1021/acs.jproteome.7b00746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707944 42]. | #Rosting C, Yu J, Cooper HJ, (2018) "High Field Asymmetric Waveform Ion Mobility Spectrometry in Nontargeted Bottom-up Proteomics of Dried Blood Spots." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707944 29707944]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00746 10.1021/acs.jproteome.7b00746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707944 42]. | ||
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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]. | ||
+ | #Simunovic F, Winninger O, Strassburg S, Koch HG, Finkenzeller G, Stark GB, Lampert FM, (2019) "Increased differentiation and production of extracellular matrix components of primary human osteoblasts after cocultivation with endothelial cells: A quantitative proteomics approach." <i>J Cell Biochem</i> <b>120</b>(1):396–404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126049 30126049]; doi: [https://dx.doi.org/10.1002/jcb.27394 10.1002/jcb.27394]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126049 20]. | ||
#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]. | #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]. | ||
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#Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC, Jungmann R, Zeigerer A, Borner GHH, Mann M, (2018) "Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis." <i>Dev Cell</i> <b>47</b>(2):205–221.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352176 30352176]; doi: [https://dx.doi.org/10.1016/j.devcel.2018.09.017 10.1016/j.devcel.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352176 134]. | #Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC, Jungmann R, Zeigerer A, Borner GHH, Mann M, (2018) "Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis." <i>Dev Cell</i> <b>47</b>(2):205–221.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352176 30352176]; doi: [https://dx.doi.org/10.1016/j.devcel.2018.09.017 10.1016/j.devcel.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352176 134]. | ||
#van Mierlo G, Wester RA, Marks H, (2018) "Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state." <i>Stem Cell Res</i> <b>33</b>:135–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352361 30352361]; doi: [https://dx.doi.org/10.1016/j.scr.2018.09.017 10.1016/j.scr.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352361 6]. | #van Mierlo G, Wester RA, Marks H, (2018) "Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state." <i>Stem Cell Res</i> <b>33</b>:135–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352361 30352361]; doi: [https://dx.doi.org/10.1016/j.scr.2018.09.017 10.1016/j.scr.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352361 6]. | ||
+ | #Serra A, Gallart-Palau X, Park JE, Lim GGY, Lim KL, Ho HH, Tam JP, Sze SK, (2018) "Vascular Bed Molecular Profiling by Differential Systemic Decellularization In Vivo." <i>Arterioscler Thromb Vasc Biol</i> <b>38</b>(10):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30354219 30354219]; doi: [https://dx.doi.org/10.1161/ATVBAHA.118.311552 10.1161/ATVBAHA.118.311552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30354219 16]. | ||
#Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | #Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | ||
#Tamminen M, Betz A, Pereira AL, Thali M, Matthews B, Suter MJ, Narwani A, (2018) "Proteome evolution under non-substitutable resource limitation." <i>Nat Commun</i> <b>9</b>(1):4650; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30405128 30405128]; doi: [https://dx.doi.org/10.1038/s41467-018-07106-z 10.1038/s41467-018-07106-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30405128 32]. | #Tamminen M, Betz A, Pereira AL, Thali M, Matthews B, Suter MJ, Narwani A, (2018) "Proteome evolution under non-substitutable resource limitation." <i>Nat Commun</i> <b>9</b>(1):4650; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30405128 30405128]; doi: [https://dx.doi.org/10.1038/s41467-018-07106-z 10.1038/s41467-018-07106-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30405128 32]. | ||
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#Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Gedeao V, Ndung'u J, Boudot C, Bisser S, Courtioux B, (2018) "Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30414516 30414516]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.11.005 10.1016/j.jprot.2018.11.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30414516 40]. | #Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Gedeao V, Ndung'u J, Boudot C, Bisser S, Courtioux B, (2018) "Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30414516 30414516]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.11.005 10.1016/j.jprot.2018.11.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30414516 40]. | ||
#Gontan C, Mira-Bontenbal H, Magaraki A, Dupont C, Barakat TS, Rentmeester E, Demmers J, Gribnau J, (2018) "REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice." <i>Nat Commun</i> <b>9</b>(1):4752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30420655 30420655]; doi: [https://dx.doi.org/10.1038/s41467-018-07060-w 10.1038/s41467-018-07060-w]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30420655 120]. | #Gontan C, Mira-Bontenbal H, Magaraki A, Dupont C, Barakat TS, Rentmeester E, Demmers J, Gribnau J, (2018) "REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice." <i>Nat Commun</i> <b>9</b>(1):4752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30420655 30420655]; doi: [https://dx.doi.org/10.1038/s41467-018-07060-w 10.1038/s41467-018-07060-w]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30420655 120]. | ||
+ | #Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G, (2018) "LZTR1 is a regulator of RAS ubiquitination and signaling." <i>Science</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30442766 30442766]; doi: [https://dx.doi.org/10.1126/science.aap8210 10.1126/science.aap8210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30442766 20]. | ||
+ | #Cominetti O, Núñez Galindo A, Corthésy J, Valsesia A, Irincheeva I, Kussmann M, Saris WHM, Astrup A, McPherson R, Harper ME, Dent R, Hager J, Dayon L, (2018) "Obesity shows preserved plasma proteome in large independent clinical cohorts." <i>Sci Rep</i> <b>8</b>(1):16981; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30451909 30451909]; doi: [https://dx.doi.org/10.1038/s41598-018-35321-7 10.1038/s41598-018-35321-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30451909 318]. | ||
+ | #Cavanagh JP, Pain M, Askarian F, Bruun JA, Urbarova I, Wai SN, Schmidt F, Johannessen M, (2018) "Comparative exoproteome profiling of an invasive and a commensal Staphylococcus haemolyticus isolate." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30472255 30472255]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.11.013 10.1016/j.jprot.2018.11.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30472255 12]. | ||
+ | #Zhu J, Garrigues L, Van den Toorn H, Stahl B, Heck AJR, (2018) "Discovery and quantification of non-human proteins in human milk." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30489082 30489082]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00550 10.1021/acs.jproteome.8b00550]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30489082 37]. | ||
+ | #Back S, Gorman AW, Vogel C, Silva GM, (2018) "Site-specific K63 ubiquitinomics provides insights into translation regulation under stress." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30489083 30489083]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00623 10.1021/acs.jproteome.8b00623]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30489083 20]. | ||
+ | #Novo D, Heath N, Mitchell L, Caligiuri G, MacFarlane A, Reijmer D, Charlton L, Knight J, Calka M, McGhee E, Dornier E, Sumpton D, Mason S, Echard A, Klinkert K, Secklehner J, Kruiswijk F, Vousden K, Macpherson IR, Blyth K, Bailey P, Yin H, Carlin LM, Morton J, Zanivan S, Norman JC, (2018) "Mutant p53s generate pro-invasive niches by influencing exosome podocalyxin levels." <i>Nat Commun</i> <b>9</b>(1):5069; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30498210 30498210]; doi: [https://dx.doi.org/10.1038/s41467-018-07339-y 10.1038/s41467-018-07339-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30498210 2]. | ||
+ | #Giovani PA, Salmon CR, Martins L, Leme AFP, Puppin-Rontani RM, Mofatto LS, Nociti FH Jr, Kantovitz KR, (2018) "Membrane proteome characterization of periodontal ligament cell sets from deciduous and permanent teeth." <i>J Periodontol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30499115 30499115]; doi: [https://dx.doi.org/10.1002/JPER.18-0217 10.1002/JPER.18-0217]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30499115 6]. | ||
+ | #Gruhlke MCH, Antelmann H, Bernhardt J, Kloubert V, Rink L, Slusarenko AJ, (2018) "The human allicin-proteome: S-thioallylation of proteins by the garlic defence substance allicin and its biological effects." <i>Free Radic Biol Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30500420 30500420]; doi: [https://dx.doi.org/10.1016/j.freeradbiomed.2018.11.022 10.1016/j.freeradbiomed.2018.11.022]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30500420 24]. | ||
+ | #Wolf A, Liesinger L, Spoerk S, Schittmayer M, Lang-Loidolt D, Birner-Gruenberger R, Tomazic PV, (2018) "Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study." <i>Sci Rep</i> <b>8</b>(1):17554; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30510230 30510230]; doi: [https://dx.doi.org/10.1038/s41598-018-35776-8 10.1038/s41598-018-35776-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30510230 21]. | ||
+ | #Tascher G, Gerbaix M, Maes P, Chazarin B, Ghislin S, Antropova E, Vassilieva G, Ouzren-Zarhloul N, Gauquelin-Koch G, Vico L, Frippiat JP, Bertile F, (2018) "Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth." <i>FASEB J</i> <b></b>:fj201801463R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30521760 30521760]; doi: [https://dx.doi.org/10.1096/fj.201801463R 10.1096/fj.201801463R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30521760 36]. |
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 December 16, 2018.