Line 27: | Line 27: | ||
==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | 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 Sept 18, 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]. | ||
#Liu T, <i>et al.</i> (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." <i>Anal Chem</i> <b>76</b>(18):5345–53; PMID: [https://pubmed.ncbi.nlm.nih.gov/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/15362891 6]. | #Liu T, <i>et al.</i> (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." <i>Anal Chem</i> <b>76</b>(18):5345–53; PMID: [https://pubmed.ncbi.nlm.nih.gov/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/15362891 6]. | ||
Line 2,343: | Line 2,342: | ||
#Drummond E, <i>et al.</i> (2020) "Phosphorylated tau interactome in the human Alzheimer's disease brain." <i>Brain</i> <b>143</b>(9):2803–2817; PMID: [https://pubmed.ncbi.nlm.nih.gov/32812023 32812023]; doi: [https://dx.doi.org/10.1093/brain/awaa223 10.1093/brain/awaa223]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32812023 27]. | #Drummond E, <i>et al.</i> (2020) "Phosphorylated tau interactome in the human Alzheimer's disease brain." <i>Brain</i> <b>143</b>(9):2803–2817; PMID: [https://pubmed.ncbi.nlm.nih.gov/32812023 32812023]; doi: [https://dx.doi.org/10.1093/brain/awaa223 10.1093/brain/awaa223]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32812023 27]. | ||
#Pang CNI, <i>et al.</i> (2020) "Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard <i>Saccharomyces cerevisiae</i> Protein Complexes." <i>Mol Cell Proteomics</i> <b>19</b>(11):1876–1895; PMID: [https://pubmed.ncbi.nlm.nih.gov/32817346 32817346]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002154 10.1074/mcp.RA120.002154]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32817346 72]. | #Pang CNI, <i>et al.</i> (2020) "Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard <i>Saccharomyces cerevisiae</i> Protein Complexes." <i>Mol Cell Proteomics</i> <b>19</b>(11):1876–1895; PMID: [https://pubmed.ncbi.nlm.nih.gov/32817346 32817346]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002154 10.1074/mcp.RA120.002154]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32817346 72]. | ||
+ | #Tahir M, <i>et al.</i> (2020) "Phosphoproteomic Analysis of Rat Neutrophils Shows the Effect of Intestinal Ischemia/Reperfusion and Preconditioning on Kinases and Phosphatases." <i>Int J Mol Sci</i> <b>21</b>(16):; PMID: [https://pubmed.ncbi.nlm.nih.gov/32823483 32823483]; doi: [https://dx.doi.org/10.3390/ijms21165799 10.3390/ijms21165799]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32823483 33]. | ||
#Maffioli E, <i>et al.</i> (2020) "Proteomic Analysis Reveals a Mitochondrial Remodeling of βTC3 Cells in Response to Nanotopography." <i>Front Cell Dev Biol</i> <b>8</b>:508; PMID: [https://pubmed.ncbi.nlm.nih.gov/32850772 32850772]; doi: [https://dx.doi.org/10.3389/fcell.2020.00508 10.3389/fcell.2020.00508]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32850772 9]. | #Maffioli E, <i>et al.</i> (2020) "Proteomic Analysis Reveals a Mitochondrial Remodeling of βTC3 Cells in Response to Nanotopography." <i>Front Cell Dev Biol</i> <b>8</b>:508; PMID: [https://pubmed.ncbi.nlm.nih.gov/32850772 32850772]; doi: [https://dx.doi.org/10.3389/fcell.2020.00508 10.3389/fcell.2020.00508]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32850772 9]. | ||
#Werner AC, <i>et al.</i> (2020) "Coronin 1B Controls Endothelial Actin Dynamics at Cell-Cell Junctions and Is Required for Endothelial Network Assembly." <i>Front Cell Dev Biol</i> <b>8</b>:708; PMID: [https://pubmed.ncbi.nlm.nih.gov/32850828 32850828]; doi: [https://dx.doi.org/10.3389/fcell.2020.00708 10.3389/fcell.2020.00708]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32850828 8]. | #Werner AC, <i>et al.</i> (2020) "Coronin 1B Controls Endothelial Actin Dynamics at Cell-Cell Junctions and Is Required for Endothelial Network Assembly." <i>Front Cell Dev Biol</i> <b>8</b>:708; PMID: [https://pubmed.ncbi.nlm.nih.gov/32850828 32850828]; doi: [https://dx.doi.org/10.3389/fcell.2020.00708 10.3389/fcell.2020.00708]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32850828 8]. | ||
Line 2,555: | Line 2,555: | ||
#Smyth SP, <i>et al.</i> (2022) "Elucidation of the protein composition of mouse seminal vesicle fluid." <i>Proteomics</i> <b></b>:e2100227; PMID: [https://pubmed.ncbi.nlm.nih.gov/35014747 35014747]; doi: [https://dx.doi.org/10.1002/pmic.202100227 10.1002/pmic.202100227]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35014747 5]. | #Smyth SP, <i>et al.</i> (2022) "Elucidation of the protein composition of mouse seminal vesicle fluid." <i>Proteomics</i> <b></b>:e2100227; PMID: [https://pubmed.ncbi.nlm.nih.gov/35014747 35014747]; doi: [https://dx.doi.org/10.1002/pmic.202100227 10.1002/pmic.202100227]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35014747 5]. | ||
#Oom AL, <i>et al.</i> (2022) "Comparative Analysis of T Cell Spatial Proteomics and the Influence of HIV Expression." <i>Mol Cell Proteomics</i> <b></b>:100194; PMID: [https://pubmed.ncbi.nlm.nih.gov/35017099 35017099]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100194 10.1016/j.mcpro.2022.100194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35017099 12]. | #Oom AL, <i>et al.</i> (2022) "Comparative Analysis of T Cell Spatial Proteomics and the Influence of HIV Expression." <i>Mol Cell Proteomics</i> <b></b>:100194; PMID: [https://pubmed.ncbi.nlm.nih.gov/35017099 35017099]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100194 10.1016/j.mcpro.2022.100194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35017099 12]. | ||
+ | #Li X, <i>et al.</i> (2022) "Mitochondria shed their outer membrane in response to infection-induced stress." <i>Science</i> <b>375</b>(6577):eabi4343; PMID: [https://pubmed.ncbi.nlm.nih.gov/35025629 35025629]; doi: [https://dx.doi.org/10.1126/science.abi4343 10.1126/science.abi4343]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35025629 86]. | ||
#Xu H, <i>et al.</i> (2022) "Proteomic profiling identifies novel diagnostic biomarkers and molecular subtypes for mucinous tubular and spindle cell carcinoma of the kidney." <i>J Pathol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35043389 35043389]; doi: [https://dx.doi.org/10.1002/path.5869 10.1002/path.5869]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35043389 5]. | #Xu H, <i>et al.</i> (2022) "Proteomic profiling identifies novel diagnostic biomarkers and molecular subtypes for mucinous tubular and spindle cell carcinoma of the kidney." <i>J Pathol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35043389 35043389]; doi: [https://dx.doi.org/10.1002/path.5869 10.1002/path.5869]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35043389 5]. | ||
#Erber L, <i>et al.</i> (2022) "Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells." <i>Molecules</i> <b>27</b>(2):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35056799 35056799]; doi: [https://dx.doi.org/10.3390/molecules27020484 10.3390/molecules27020484]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35056799 24]. | #Erber L, <i>et al.</i> (2022) "Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells." <i>Molecules</i> <b>27</b>(2):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35056799 35056799]; doi: [https://dx.doi.org/10.3390/molecules27020484 10.3390/molecules27020484]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35056799 24]. | ||
Line 2,580: | Line 2,581: | ||
#Ubaida-Mohien C, <i>et al.</i> (2022) "Unbiased proteomics, histochemistry, and mitochondrial DNA copy number reveal better mitochondrial health in muscle of high functioning octogenarians." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35404238 35404238]; doi: [https://dx.doi.org/10.7554/eLife.74335 10.7554/eLife.74335]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35404238 98]. | #Ubaida-Mohien C, <i>et al.</i> (2022) "Unbiased proteomics, histochemistry, and mitochondrial DNA copy number reveal better mitochondrial health in muscle of high functioning octogenarians." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35404238 35404238]; doi: [https://dx.doi.org/10.7554/eLife.74335 10.7554/eLife.74335]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35404238 98]. | ||
#Agajanian MJ, <i>et al.</i> (2022) "Protein proximity networks and functional evaluation of the casein kinase 1 gamma family reveal unique roles for CK1γ3 in WNT signaling." <i>J Biol Chem</i> <b>298</b>(6):101986; PMID: [https://pubmed.ncbi.nlm.nih.gov/35487243 35487243]; doi: [https://dx.doi.org/10.1016/j.jbc.2022.101986 10.1016/j.jbc.2022.101986]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35487243 28]. | #Agajanian MJ, <i>et al.</i> (2022) "Protein proximity networks and functional evaluation of the casein kinase 1 gamma family reveal unique roles for CK1γ3 in WNT signaling." <i>J Biol Chem</i> <b>298</b>(6):101986; PMID: [https://pubmed.ncbi.nlm.nih.gov/35487243 35487243]; doi: [https://dx.doi.org/10.1016/j.jbc.2022.101986 10.1016/j.jbc.2022.101986]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35487243 28]. | ||
+ | #Hardesty J, <i>et al.</i> (2022) "Hepatic Protein and Phosphoprotein Signatures of Alcohol-Associated Cirrhosis and Hepatitis." <i>Am J Pathol</i> <b>192</b>(7):1066–1082; PMID: [https://pubmed.ncbi.nlm.nih.gov/35490715 35490715]; doi: [https://dx.doi.org/10.1016/j.ajpath.2022.04.004 10.1016/j.ajpath.2022.04.004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35490715 54]. | ||
#Fernando M, <i>et al.</i> (2022) "Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin." <i>Stem Cell Reports</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35523177 35523177]; doi: [https://dx.doi.org/10.1016/j.stemcr.2022.04.003 10.1016/j.stemcr.2022.04.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35523177 117]. | #Fernando M, <i>et al.</i> (2022) "Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin." <i>Stem Cell Reports</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35523177 35523177]; doi: [https://dx.doi.org/10.1016/j.stemcr.2022.04.003 10.1016/j.stemcr.2022.04.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35523177 117]. | ||
#Levitsky LI, <i>et al.</i> (2022) "Validating Amino Acid Variants in Proteogenomics Using Sequence Coverage by Multiple Reads." <i>J Proteome Res</i> <b>21</b>(6):1438–1448; PMID: [https://pubmed.ncbi.nlm.nih.gov/35536917 35536917]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00033 10.1021/acs.jproteome.2c00033]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35536917 9]. | #Levitsky LI, <i>et al.</i> (2022) "Validating Amino Acid Variants in Proteogenomics Using Sequence Coverage by Multiple Reads." <i>J Proteome Res</i> <b>21</b>(6):1438–1448; PMID: [https://pubmed.ncbi.nlm.nih.gov/35536917 35536917]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00033 10.1021/acs.jproteome.2c00033]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35536917 9]. | ||
+ | #Liu X, <i>et al.</i> (2022) "Profiling Yeast Deletion Strains Using Sample Multiplexing and Network-Based Analyses." <i>J Proteome Res</i> <b>21</b>(6):1525–1536; PMID: [https://pubmed.ncbi.nlm.nih.gov/35544774 35544774]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00137 10.1021/acs.jproteome.2c00137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35544774 5]. | ||
+ | #Wang M, <i>et al.</i> (2022) "Gefitinib and fostamatinib target EGFR and SYK to attenuate silicosis: a multi-omics study with drug exploration." <i>Signal Transduct Target Ther</i> <b>7</b>(1):157; PMID: [https://pubmed.ncbi.nlm.nih.gov/35551173 35551173]; doi: [https://dx.doi.org/10.1038/s41392-022-00959-3 10.1038/s41392-022-00959-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35551173 37]. | ||
#Spaan AN, <i>et al.</i> (2022) "Human OTULIN haploinsufficiency impairs cell-intrinsic immunity to staphylococcal α-toxin." <i>Science</i> <b>376</b>(6599):eabm6380; PMID: [https://pubmed.ncbi.nlm.nih.gov/35587511 35587511]; doi: [https://dx.doi.org/10.1126/science.abm6380 10.1126/science.abm6380]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35587511 48]. | #Spaan AN, <i>et al.</i> (2022) "Human OTULIN haploinsufficiency impairs cell-intrinsic immunity to staphylococcal α-toxin." <i>Science</i> <b>376</b>(6599):eabm6380; PMID: [https://pubmed.ncbi.nlm.nih.gov/35587511 35587511]; doi: [https://dx.doi.org/10.1126/science.abm6380 10.1126/science.abm6380]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35587511 48]. | ||
#Mari T, <i>et al.</i> (2022) "In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets." <i>J Proteome Res</i> <b>21</b>(6):1575–1587; PMID: [https://pubmed.ncbi.nlm.nih.gov/35608653 35608653]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00198 10.1021/acs.jproteome.2c00198]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35608653 13]. | #Mari T, <i>et al.</i> (2022) "In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets." <i>J Proteome Res</i> <b>21</b>(6):1575–1587; PMID: [https://pubmed.ncbi.nlm.nih.gov/35608653 35608653]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00198 10.1021/acs.jproteome.2c00198]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35608653 13]. | ||
Line 2,592: | Line 2,596: | ||
#Ebeling MC, <i>et al.</i> (2022) "Inflammasome Activation in Retinal Pigment Epithelium from Human Donors with Age-Related Macular Degeneration." <i>Cells</i> <b>11</b>(13):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35805159 35805159]; doi: [https://dx.doi.org/10.3390/cells11132075 10.3390/cells11132075]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35805159 77]. | #Ebeling MC, <i>et al.</i> (2022) "Inflammasome Activation in Retinal Pigment Epithelium from Human Donors with Age-Related Macular Degeneration." <i>Cells</i> <b>11</b>(13):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35805159 35805159]; doi: [https://dx.doi.org/10.3390/cells11132075 10.3390/cells11132075]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35805159 77]. | ||
#Ledoult E, <i>et al.</i> (2022) "Simple gene signature to assess murine fibroblast polarization." <i>Sci Rep</i> <b>12</b>(1):11748; PMID: [https://pubmed.ncbi.nlm.nih.gov/35817787 35817787]; doi: [https://dx.doi.org/10.1038/s41598-022-15640-6 10.1038/s41598-022-15640-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35817787 15]. | #Ledoult E, <i>et al.</i> (2022) "Simple gene signature to assess murine fibroblast polarization." <i>Sci Rep</i> <b>12</b>(1):11748; PMID: [https://pubmed.ncbi.nlm.nih.gov/35817787 35817787]; doi: [https://dx.doi.org/10.1038/s41598-022-15640-6 10.1038/s41598-022-15640-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35817787 15]. | ||
- | #Havugimana PC, <i>et al.</i> (2022) "Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery." <i>Nat Commun</i> <b>13</b>(1):4043; PMID: [https://pubmed.ncbi.nlm.nih.gov/35831314 35831314]; doi: [https://dx.doi.org/10.1038/s41467-022-31809-z 10.1038/s41467-022-31809-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35831314 | + | #Havugimana PC, <i>et al.</i> (2022) "Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery." <i>Nat Commun</i> <b>13</b>(1):4043; PMID: [https://pubmed.ncbi.nlm.nih.gov/35831314 35831314]; doi: [https://dx.doi.org/10.1038/s41467-022-31809-z 10.1038/s41467-022-31809-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35831314 192]. |
#Wrobel L, <i>et al.</i> (2022) "Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance." <i>Nat Commun</i> <b>13</b>(1):4146; PMID: [https://pubmed.ncbi.nlm.nih.gov/35842429 35842429]; doi: [https://dx.doi.org/10.1038/s41467-022-31905-0 10.1038/s41467-022-31905-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35842429 12]. | #Wrobel L, <i>et al.</i> (2022) "Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance." <i>Nat Commun</i> <b>13</b>(1):4146; PMID: [https://pubmed.ncbi.nlm.nih.gov/35842429 35842429]; doi: [https://dx.doi.org/10.1038/s41467-022-31905-0 10.1038/s41467-022-31905-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35842429 12]. | ||
+ | #Yu R, <i>et al.</i> (2022) "LncRNA CTBP1-DT-encoded microprotein DDUP sustains DNA damage response signalling to trigger dual DNA repair mechanisms." <i>Nucleic Acids Res</i> <b>50</b>(14):8060–8079; PMID: [https://pubmed.ncbi.nlm.nih.gov/35849344 35849344]; doi: [https://dx.doi.org/10.1093/nar/gkac611 10.1093/nar/gkac611]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35849344 2]. | ||
+ | #Sridharan S, <i>et al.</i> (2022) "Systematic discovery of biomolecular condensate-specific protein phosphorylation." <i>Nat Chem Biol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35864335 35864335]; doi: [https://dx.doi.org/10.1038/s41589-022-01062-y 10.1038/s41589-022-01062-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35864335 60]. | ||
#Rademaker G, <i>et al.</i> (2022) "Paladin, overexpressed in colon cancer, is required for actin polymerisation and liver metastasis dissemination." <i>Oncogenesis</i> <b>11</b>(1):42; PMID: [https://pubmed.ncbi.nlm.nih.gov/35882839 35882839]; doi: [https://dx.doi.org/10.1038/s41389-022-00416-4 10.1038/s41389-022-00416-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35882839 18]. | #Rademaker G, <i>et al.</i> (2022) "Paladin, overexpressed in colon cancer, is required for actin polymerisation and liver metastasis dissemination." <i>Oncogenesis</i> <b>11</b>(1):42; PMID: [https://pubmed.ncbi.nlm.nih.gov/35882839 35882839]; doi: [https://dx.doi.org/10.1038/s41389-022-00416-4 10.1038/s41389-022-00416-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35882839 18]. | ||
#Vadnjal N, <i>et al.</i> (2022) "Proteomic analysis of the actin cortex in interphase and mitosis." <i>J Cell Sci</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35892282 35892282]; doi: [https://dx.doi.org/10.1242/jcs.259993 10.1242/jcs.259993]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35892282 36]. | #Vadnjal N, <i>et al.</i> (2022) "Proteomic analysis of the actin cortex in interphase and mitosis." <i>J Cell Sci</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35892282 35892282]; doi: [https://dx.doi.org/10.1242/jcs.259993 10.1242/jcs.259993]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35892282 36]. | ||
+ | #Ferraro G, <i>et al.</i> (2022) "A Proteomic Platform Unveils the Brain Glycogen Phosphorylase as a Potential Therapeutic Target for Glioblastoma Multiforme." <i>Int J Mol Sci</i> <b>23</b>(15):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35897773 35897773]; doi: [https://dx.doi.org/10.3390/ijms23158200 10.3390/ijms23158200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35897773 104]. | ||
+ | #Li H, <i>et al.</i> (2022) "Global phosphoproteomic analysis identified key kinases regulating male meiosis in mouse." <i>Cell Mol Life Sci</i> <b>79</b>(8):467; PMID: [https://pubmed.ncbi.nlm.nih.gov/35930080 35930080]; doi: [https://dx.doi.org/10.1007/s00018-022-04507-8 10.1007/s00018-022-04507-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35930080 45]. | ||
+ | #Zhang Y, <i>et al.</i> (2022) "Lysine Acetylome Profiling Reveals Diverse Functions of Acetylation in Deinococcus radiodurans." <i>Microbiol Spectr</i> <b></b>:e0101621; PMID: [https://pubmed.ncbi.nlm.nih.gov/35972276 35972276]; doi: [https://dx.doi.org/10.1128/spectrum.01016-21 10.1128/spectrum.01016-21]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35972276 18]. | ||
+ | #Ji JX, <i>et al.</i> (2022) "The proteome of clear cell ovarian carcinoma." <i>J Pathol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36031730 36031730]; doi: [https://dx.doi.org/10.1002/path.6006 10.1002/path.6006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36031730 17]. | ||
+ | #Pirhonen J, <i>et al.</i> (2022) "Lipid metabolic reprogramming extends beyond histological tumor demarcations in operable human pancreatic cancer." <i>Cancer Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36054547 36054547]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-22-0396 10.1158/0008-5472.CAN-22-0396]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36054547 64]. |
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 Sept 18, 2022.