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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 14, 2022. |
#Lipton MS, <i>et al.</i> (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: [https://pubmed.ncbi.nlm.nih.gov/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, <i>et al.</i> (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: [https://pubmed.ncbi.nlm.nih.gov/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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#Wei W, <i>et al.</i> (2016) "Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer." <i>J Proteome Res</i> <b>15</b>(11):3988–3997; PMID: [https://pubmed.ncbi.nlm.nih.gov/27535590 27535590]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00390 10.1021/acs.jproteome.6b00390]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535590 150]. | #Wei W, <i>et al.</i> (2016) "Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer." <i>J Proteome Res</i> <b>15</b>(11):3988–3997; PMID: [https://pubmed.ncbi.nlm.nih.gov/27535590 27535590]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00390 10.1021/acs.jproteome.6b00390]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535590 150]. | ||
#Dobó J, <i>et al.</i> (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [https://pubmed.ncbi.nlm.nih.gov/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535802 6]. | #Dobó J, <i>et al.</i> (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [https://pubmed.ncbi.nlm.nih.gov/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535802 6]. | ||
- | #Zhang P, <i>et al.</i> (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [https://pubmed.ncbi.nlm.nih.gov/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27538499 | + | #Zhang P, <i>et al.</i> (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [https://pubmed.ncbi.nlm.nih.gov/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27538499 125]. |
#Walley JW, <i>et al.</i> (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [https://pubmed.ncbi.nlm.nih.gov/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27540173 10350]. | #Walley JW, <i>et al.</i> (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [https://pubmed.ncbi.nlm.nih.gov/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27540173 10350]. | ||
#Xie Y, <i>et al.</i> (2016) "Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells." <i>Sci Rep</i> <b>6</b>:31811; PMID: [https://pubmed.ncbi.nlm.nih.gov/27554326 27554326]; doi: [https://dx.doi.org/10.1038/srep31811 10.1038/srep31811]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27554326 6]. | #Xie Y, <i>et al.</i> (2016) "Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells." <i>Sci Rep</i> <b>6</b>:31811; PMID: [https://pubmed.ncbi.nlm.nih.gov/27554326 27554326]; doi: [https://dx.doi.org/10.1038/srep31811 10.1038/srep31811]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27554326 6]. | ||
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#Diaz-Vera J, <i>et al.</i> (2017) "A proteomic approach to identify endosomal cargoes controlling cancer invasiveness." <i>J Cell Sci</i> <b>130</b>(4):697–711; PMID: [https://pubmed.ncbi.nlm.nih.gov/28062852 28062852]; doi: [https://dx.doi.org/10.1242/jcs.190835 10.1242/jcs.190835]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28062852 106]. | #Diaz-Vera J, <i>et al.</i> (2017) "A proteomic approach to identify endosomal cargoes controlling cancer invasiveness." <i>J Cell Sci</i> <b>130</b>(4):697–711; PMID: [https://pubmed.ncbi.nlm.nih.gov/28062852 28062852]; doi: [https://dx.doi.org/10.1242/jcs.190835 10.1242/jcs.190835]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28062852 106]. | ||
#Pietzner M, <i>et al.</i> (2017) "Plasma proteome and metabolome characterization of an experimental human thyrotoxicosis model." <i>BMC Med</i> <b>15</b>(1):6; PMID: [https://pubmed.ncbi.nlm.nih.gov/28065164 28065164]; doi: [https://dx.doi.org/10.1186/s12916-016-0770-8 10.1186/s12916-016-0770-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28065164 80]. | #Pietzner M, <i>et al.</i> (2017) "Plasma proteome and metabolome characterization of an experimental human thyrotoxicosis model." <i>BMC Med</i> <b>15</b>(1):6; PMID: [https://pubmed.ncbi.nlm.nih.gov/28065164 28065164]; doi: [https://dx.doi.org/10.1186/s12916-016-0770-8 10.1186/s12916-016-0770-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28065164 80]. | ||
- | #Kreutz D, <i>et al.</i> (2017) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." <i>Chemistry</i> <b>23</b>(8):1881–1890; PMID: [https://pubmed.ncbi.nlm.nih.gov/28071820 28071820]; doi: [https://dx.doi.org/10.1002/chem.201604516 10.1002/chem.201604516]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28071820 | + | #Kreutz D, <i>et al.</i> (2017) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." <i>Chemistry</i> <b>23</b>(8):1881–1890; PMID: [https://pubmed.ncbi.nlm.nih.gov/28071820 28071820]; doi: [https://dx.doi.org/10.1002/chem.201604516 10.1002/chem.201604516]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28071820 120]. |
#Xing F, <i>et al.</i> (2017) "The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes." <i>Cell Rep</i> <b>18</b>(2):468–481; PMID: [https://pubmed.ncbi.nlm.nih.gov/28076790 28076790]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.037 10.1016/j.celrep.2016.12.037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28076790 60]. | #Xing F, <i>et al.</i> (2017) "The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes." <i>Cell Rep</i> <b>18</b>(2):468–481; PMID: [https://pubmed.ncbi.nlm.nih.gov/28076790 28076790]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.037 10.1016/j.celrep.2016.12.037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28076790 60]. | ||
#Loroch S, <i>et al.</i> (2017) "Alterations of the platelet proteome in type I Glanzmann thrombasthenia caused by different homozygous delG frameshift mutations in ITGA2B." <i>Thromb Haemost</i> <b>117</b>(3):556–569; PMID: [https://pubmed.ncbi.nlm.nih.gov/28078347 28078347]; doi: [https://dx.doi.org/10.1160/TH16-07-0515 10.1160/TH16-07-0515]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28078347 20]. | #Loroch S, <i>et al.</i> (2017) "Alterations of the platelet proteome in type I Glanzmann thrombasthenia caused by different homozygous delG frameshift mutations in ITGA2B." <i>Thromb Haemost</i> <b>117</b>(3):556–569; PMID: [https://pubmed.ncbi.nlm.nih.gov/28078347 28078347]; doi: [https://dx.doi.org/10.1160/TH16-07-0515 10.1160/TH16-07-0515]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28078347 20]. | ||
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#Saravanan R, <i>et al.</i> (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [https://pubmed.ncbi.nlm.nih.gov/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29030565 43]. | #Saravanan R, <i>et al.</i> (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [https://pubmed.ncbi.nlm.nih.gov/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29030565 43]. | ||
#Grenga L, <i>et al.</i> (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." <i>Front Microbiol</i> <b>8</b>:1784; PMID: [https://pubmed.ncbi.nlm.nih.gov/29033902 29033902]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01784 10.3389/fmicb.2017.01784]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29033902 1]. | #Grenga L, <i>et al.</i> (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." <i>Front Microbiol</i> <b>8</b>:1784; PMID: [https://pubmed.ncbi.nlm.nih.gov/29033902 29033902]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01784 10.3389/fmicb.2017.01784]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29033902 1]. | ||
+ | #Solanki HS, <i>et al.</i> (2018) "Cigarette smoke induces mitochondrial metabolic reprogramming in lung cells." <i>Mitochondrion</i> <b>40</b>:58–70; PMID: [https://pubmed.ncbi.nlm.nih.gov/29042306 29042306]; doi: [https://dx.doi.org/10.1016/j.mito.2017.10.002 10.1016/j.mito.2017.10.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29042306 3]. | ||
#Kugeratski FG, <i>et al.</i> (2018) "Mitogen-Activated Protein Kinase Kinase 5 Regulates Proliferation and Biosynthetic Processes in Procyclic Forms of Trypanosoma brucei." <i>J Proteome Res</i> <b>17</b>(1):108–118; PMID: [https://pubmed.ncbi.nlm.nih.gov/29043805 29043805]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00415 10.1021/acs.jproteome.7b00415]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29043805 15]. | #Kugeratski FG, <i>et al.</i> (2018) "Mitogen-Activated Protein Kinase Kinase 5 Regulates Proliferation and Biosynthetic Processes in Procyclic Forms of Trypanosoma brucei." <i>J Proteome Res</i> <b>17</b>(1):108–118; PMID: [https://pubmed.ncbi.nlm.nih.gov/29043805 29043805]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00415 10.1021/acs.jproteome.7b00415]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29043805 15]. | ||
#Bartosova M, <i>et al.</i> (2018) "Complement Activation in Peritoneal Dialysis-Induced Arteriolopathy." <i>J Am Soc Nephrol</i> <b>29</b>(1):268–282; PMID: [https://pubmed.ncbi.nlm.nih.gov/29046343 29046343]; doi: [https://dx.doi.org/10.1681/ASN.2017040436 10.1681/ASN.2017040436]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29046343 2]. | #Bartosova M, <i>et al.</i> (2018) "Complement Activation in Peritoneal Dialysis-Induced Arteriolopathy." <i>J Am Soc Nephrol</i> <b>29</b>(1):268–282; PMID: [https://pubmed.ncbi.nlm.nih.gov/29046343 29046343]; doi: [https://dx.doi.org/10.1681/ASN.2017040436 10.1681/ASN.2017040436]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29046343 2]. | ||
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#Hurcombe JA, <i>et al.</i> (2019) "Podocyte GSK3 is an evolutionarily conserved critical regulator of kidney function." <i>Nat Commun</i> <b>10</b>(1):403; PMID: [https://pubmed.ncbi.nlm.nih.gov/30679422 30679422]; doi: [https://dx.doi.org/10.1038/s41467-018-08235-1 10.1038/s41467-018-08235-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30679422 1]. | #Hurcombe JA, <i>et al.</i> (2019) "Podocyte GSK3 is an evolutionarily conserved critical regulator of kidney function." <i>Nat Commun</i> <b>10</b>(1):403; PMID: [https://pubmed.ncbi.nlm.nih.gov/30679422 30679422]; doi: [https://dx.doi.org/10.1038/s41467-018-08235-1 10.1038/s41467-018-08235-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30679422 1]. | ||
#Fornecker LM, <i>et al.</i> (2019) "Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma." <i>Sci Rep</i> <b>9</b>(1):895; PMID: [https://pubmed.ncbi.nlm.nih.gov/30696890 30696890]; doi: [https://dx.doi.org/10.1038/s41598-018-37273-4 10.1038/s41598-018-37273-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30696890 20]. | #Fornecker LM, <i>et al.</i> (2019) "Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma." <i>Sci Rep</i> <b>9</b>(1):895; PMID: [https://pubmed.ncbi.nlm.nih.gov/30696890 30696890]; doi: [https://dx.doi.org/10.1038/s41598-018-37273-4 10.1038/s41598-018-37273-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30696890 20]. | ||
+ | #Huang S, <i>et al.</i> (2019) "Comprehensive and combined omics analysis reveals factors of ischemia-reperfusion injury in liver transplantation." <i>Epigenomics</i> <b>11</b>(5):527–542; PMID: [https://pubmed.ncbi.nlm.nih.gov/30700158 30700158]; doi: [https://dx.doi.org/10.2217/epi-2018-0189 10.2217/epi-2018-0189]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30700158 3]. | ||
#Dayon L, <i>et al.</i> (2019) "Proteomes of Paired Human Cerebrospinal Fluid and Plasma: Relation to Blood-Brain Barrier Permeability in Older Adults." <i>J Proteome Res</i> <b>18</b>(3):1162–1174; PMID: [https://pubmed.ncbi.nlm.nih.gov/30702894 30702894]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00809 10.1021/acs.jproteome.8b00809]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30702894 128]. | #Dayon L, <i>et al.</i> (2019) "Proteomes of Paired Human Cerebrospinal Fluid and Plasma: Relation to Blood-Brain Barrier Permeability in Older Adults." <i>J Proteome Res</i> <b>18</b>(3):1162–1174; PMID: [https://pubmed.ncbi.nlm.nih.gov/30702894 30702894]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00809 10.1021/acs.jproteome.8b00809]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30702894 128]. | ||
#McKetney J, <i>et al.</i> (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." <i>J Proteome Res</i> <b>18</b>(3):1380–1391; PMID: [https://pubmed.ncbi.nlm.nih.gov/30735395 30735395]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00004 10.1021/acs.jproteome.9b00004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30735395 22]. | #McKetney J, <i>et al.</i> (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." <i>J Proteome Res</i> <b>18</b>(3):1380–1391; PMID: [https://pubmed.ncbi.nlm.nih.gov/30735395 30735395]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00004 10.1021/acs.jproteome.9b00004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30735395 22]. | ||
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#Cunningham DL, <i>et al.</i> (2020) "Differential responses to kinase inhibition in FGFR2-addicted triple negative breast cancer cells: a quantitative phosphoproteomics study." <i>Sci Rep</i> <b>10</b>(1):7950; PMID: [https://pubmed.ncbi.nlm.nih.gov/32409632 32409632]; doi: [https://dx.doi.org/10.1038/s41598-020-64534-y 10.1038/s41598-020-64534-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32409632 377]. | #Cunningham DL, <i>et al.</i> (2020) "Differential responses to kinase inhibition in FGFR2-addicted triple negative breast cancer cells: a quantitative phosphoproteomics study." <i>Sci Rep</i> <b>10</b>(1):7950; PMID: [https://pubmed.ncbi.nlm.nih.gov/32409632 32409632]; doi: [https://dx.doi.org/10.1038/s41598-020-64534-y 10.1038/s41598-020-64534-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32409632 377]. | ||
#van Geelen L, <i>et al.</i> (2020) "Natural brominated phenoxyphenols kill persistent and biofilm-incorporated cells of MRSA and other pathogenic bacteria." <i>Appl Microbiol Biotechnol</i> <b>104</b>(13):5985–5998; PMID: [https://pubmed.ncbi.nlm.nih.gov/32418125 32418125]; doi: [https://dx.doi.org/10.1007/s00253-020-10654-4 10.1007/s00253-020-10654-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32418125 12]. | #van Geelen L, <i>et al.</i> (2020) "Natural brominated phenoxyphenols kill persistent and biofilm-incorporated cells of MRSA and other pathogenic bacteria." <i>Appl Microbiol Biotechnol</i> <b>104</b>(13):5985–5998; PMID: [https://pubmed.ncbi.nlm.nih.gov/32418125 32418125]; doi: [https://dx.doi.org/10.1007/s00253-020-10654-4 10.1007/s00253-020-10654-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32418125 12]. | ||
- | #de la Fuente AG, <i>et al.</i> (2020) "Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing." <i>Mol Cell Proteomics</i> <b>19</b>(8):1281–1302; PMID: [https://pubmed.ncbi.nlm.nih.gov/32434922 32434922]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002102 10.1074/mcp.RA120.002102]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32434922 | + | #Maity S, <i>et al.</i> (2020) "Quantitative alterations in bovine milk proteome from healthy, subclinical and clinical mastitis during S. aureus infection." <i>J Proteomics</i> <b>223</b>:103815; PMID: [https://pubmed.ncbi.nlm.nih.gov/32423885 32423885]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103815 10.1016/j.jprot.2020.103815]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32423885 12]. |
+ | #de la Fuente AG, <i>et al.</i> (2020) "Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing." <i>Mol Cell Proteomics</i> <b>19</b>(8):1281–1302; PMID: [https://pubmed.ncbi.nlm.nih.gov/32434922 32434922]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002102 10.1074/mcp.RA120.002102]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32434922 8]. | ||
#Cervantes M, <i>et al.</i> (2020) "BMAL1 Associates with NOP58 in the Nucleolus and Contributes to Pre-rRNA Processing." <i>iScience</i> <b>23</b>(6):101151; PMID: [https://pubmed.ncbi.nlm.nih.gov/32450515 32450515]; doi: [https://dx.doi.org/10.1016/j.isci.2020.101151 10.1016/j.isci.2020.101151]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32450515 24]. | #Cervantes M, <i>et al.</i> (2020) "BMAL1 Associates with NOP58 in the Nucleolus and Contributes to Pre-rRNA Processing." <i>iScience</i> <b>23</b>(6):101151; PMID: [https://pubmed.ncbi.nlm.nih.gov/32450515 32450515]; doi: [https://dx.doi.org/10.1016/j.isci.2020.101151 10.1016/j.isci.2020.101151]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32450515 24]. | ||
#Van JAD, <i>et al.</i> (2020) "Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes." <i>PLoS One</i> <b>15</b>(5):e0233639; PMID: [https://pubmed.ncbi.nlm.nih.gov/32453760 32453760]; doi: [https://dx.doi.org/10.1371/journal.pone.0233639 10.1371/journal.pone.0233639]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32453760 90]. | #Van JAD, <i>et al.</i> (2020) "Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes." <i>PLoS One</i> <b>15</b>(5):e0233639; PMID: [https://pubmed.ncbi.nlm.nih.gov/32453760 32453760]; doi: [https://dx.doi.org/10.1371/journal.pone.0233639 10.1371/journal.pone.0233639]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32453760 90]. | ||
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#Yuan S, <i>et al.</i> (2021) "Translatomic profiling reveals novel self-restricting virus-host interactions during HBV infection." <i>J Hepatol</i> <b>75</b>(1):74–85; PMID: [https://pubmed.ncbi.nlm.nih.gov/33621634 33621634]; doi: [https://dx.doi.org/10.1016/j.jhep.2021.02.009 10.1016/j.jhep.2021.02.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33621634 3]. | #Yuan S, <i>et al.</i> (2021) "Translatomic profiling reveals novel self-restricting virus-host interactions during HBV infection." <i>J Hepatol</i> <b>75</b>(1):74–85; PMID: [https://pubmed.ncbi.nlm.nih.gov/33621634 33621634]; doi: [https://dx.doi.org/10.1016/j.jhep.2021.02.009 10.1016/j.jhep.2021.02.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33621634 3]. | ||
#Gassaway BM, <i>et al.</i> (2021) "Categorization of Phosphorylation Site Behavior during the Diauxic Shift in <i>Saccharomyces cerevisiae</i>." <i>J Proteome Res</i> <b>20</b>(5):2487–2496; PMID: [https://pubmed.ncbi.nlm.nih.gov/33630598 33630598]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00943 10.1021/acs.jproteome.0c00943]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33630598 42]. | #Gassaway BM, <i>et al.</i> (2021) "Categorization of Phosphorylation Site Behavior during the Diauxic Shift in <i>Saccharomyces cerevisiae</i>." <i>J Proteome Res</i> <b>20</b>(5):2487–2496; PMID: [https://pubmed.ncbi.nlm.nih.gov/33630598 33630598]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00943 10.1021/acs.jproteome.0c00943]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33630598 42]. | ||
+ | #Van Bergen MGJM, <i>et al.</i> (2021) "Specific proteome changes in platelets from individuals with GATA1-, GFI1B-, and RUNX1-linked bleeding disorders." <i>Blood</i> <b>138</b>(1):86–90; PMID: [https://pubmed.ncbi.nlm.nih.gov/33690840 33690840]; doi: [https://dx.doi.org/10.1182/blood.2020008118 10.1182/blood.2020008118]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33690840 37]. | ||
#Kalaora S, <i>et al.</i> (2021) "Identification of bacteria-derived HLA-bound peptides in melanoma." <i>Nature</i> <b>592</b>(7852):138–143; PMID: [https://pubmed.ncbi.nlm.nih.gov/33731925 33731925]; doi: [https://dx.doi.org/10.1038/s41586-021-03368-8 10.1038/s41586-021-03368-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33731925 153]. | #Kalaora S, <i>et al.</i> (2021) "Identification of bacteria-derived HLA-bound peptides in melanoma." <i>Nature</i> <b>592</b>(7852):138–143; PMID: [https://pubmed.ncbi.nlm.nih.gov/33731925 33731925]; doi: [https://dx.doi.org/10.1038/s41586-021-03368-8 10.1038/s41586-021-03368-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33731925 153]. | ||
#Schmid D, <i>et al.</i> (2021) "Diagnostic biomarkers from proteomic characterization of cerebrospinal fluid in patients with brain malignancies." <i>J Neurochem</i> <b>158</b>(2):522–538; PMID: [https://pubmed.ncbi.nlm.nih.gov/33735443 33735443]; doi: [https://dx.doi.org/10.1111/jnc.15350 10.1111/jnc.15350]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33735443 299]. | #Schmid D, <i>et al.</i> (2021) "Diagnostic biomarkers from proteomic characterization of cerebrospinal fluid in patients with brain malignancies." <i>J Neurochem</i> <b>158</b>(2):522–538; PMID: [https://pubmed.ncbi.nlm.nih.gov/33735443 33735443]; doi: [https://dx.doi.org/10.1111/jnc.15350 10.1111/jnc.15350]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33735443 299]. | ||
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#Krishnan RK, <i>et al.</i> (2021) "Revisiting the Role of <i>ß</i>-Tubulin in <i>Drosophila</i> Development: <i>β-tubulin60D</i> is not an Essential Gene, and its Novel <i>Pin</i> <sup><i>1</i></sup> Allele has a Tissue-Specific Dominant-Negative Impact." <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [https://pubmed.ncbi.nlm.nih.gov/35111755 35111755]; doi: [https://dx.doi.org/10.3389/fcell.2021.787976 10.3389/fcell.2021.787976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35111755 6]. | #Krishnan RK, <i>et al.</i> (2021) "Revisiting the Role of <i>ß</i>-Tubulin in <i>Drosophila</i> Development: <i>β-tubulin60D</i> is not an Essential Gene, and its Novel <i>Pin</i> <sup><i>1</i></sup> Allele has a Tissue-Specific Dominant-Negative Impact." <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [https://pubmed.ncbi.nlm.nih.gov/35111755 35111755]; doi: [https://dx.doi.org/10.3389/fcell.2021.787976 10.3389/fcell.2021.787976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35111755 6]. | ||
#Correll VL, <i>et al.</i> (2022) "Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis." <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [https://pubmed.ncbi.nlm.nih.gov/35119778 35119778]; doi: [https://dx.doi.org/10.1002/jev2.12184 10.1002/jev2.12184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35119778 9]. | #Correll VL, <i>et al.</i> (2022) "Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis." <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [https://pubmed.ncbi.nlm.nih.gov/35119778 35119778]; doi: [https://dx.doi.org/10.1002/jev2.12184 10.1002/jev2.12184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35119778 9]. | ||
- | #Wang C, <i>et al.</i> (2022) "Stat4 rs7574865 polymorphism promotes the occurrence and progression of hepatocellular carcinoma via the Stat4/CYP2E1/FGL2 pathway." <i>Cell Death Dis</i> <b>13</b>(2):130; PMID: [https://pubmed.ncbi.nlm.nih.gov/35136014 35136014]; doi: [https://dx.doi.org/10.1038/s41419-022-04584-4 10.1038/s41419-022-04584-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35136014 | + | #Wang C, <i>et al.</i> (2022) "Stat4 rs7574865 polymorphism promotes the occurrence and progression of hepatocellular carcinoma via the Stat4/CYP2E1/FGL2 pathway." <i>Cell Death Dis</i> <b>13</b>(2):130; PMID: [https://pubmed.ncbi.nlm.nih.gov/35136014 35136014]; doi: [https://dx.doi.org/10.1038/s41419-022-04584-4 10.1038/s41419-022-04584-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35136014 83]. |
#Rezaei-Gazik M, <i>et al.</i> (2022) "Direct visualization of pre-protamine 2 detects protamine assembly failures and predicts ICSI success." <i>Mol Hum Reprod</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35150275 35150275]; doi: [https://dx.doi.org/10.1093/molehr/gaac004 10.1093/molehr/gaac004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35150275 24]. | #Rezaei-Gazik M, <i>et al.</i> (2022) "Direct visualization of pre-protamine 2 detects protamine assembly failures and predicts ICSI success." <i>Mol Hum Reprod</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35150275 35150275]; doi: [https://dx.doi.org/10.1093/molehr/gaac004 10.1093/molehr/gaac004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35150275 24]. | ||
+ | #Thim-Uam A, <i>et al.</i> (2022) "Enhanced Bacteremia in Dextran Sulfate-Induced Colitis in Splenectomy Mice Correlates with Gut Dysbiosis and LPS Tolerance." <i>Int J Mol Sci</i> <b>23</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35163596 35163596]; doi: [https://dx.doi.org/10.3390/ijms23031676 10.3390/ijms23031676]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35163596 3]. | ||
+ | #COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium. Electronic address: julian.knight@well.ox.ac.uk., <i>et al.</i> (2022) "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity." <i>Cell</i> <b>185</b>(5):916–938.e58; PMID: [https://pubmed.ncbi.nlm.nih.gov/35216673 35216673]; doi: [https://dx.doi.org/10.1016/j.cell.2022.01.012 10.1016/j.cell.2022.01.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35216673 559]. |
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 datasets/papers contain serious errors in their metadata/methods sections. When using data from repositories, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methods, etc.) that may impact on your use of the data. We have corrected for as many of these errors as we could detect, but there is no way to be sure that we found them all. When attempting to analyze or reproduce results, keep in mind the likelihood that key parts of the experimental methods may have been recorded incorrectly in the associated metadata or manuscript.
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 14, 2022.