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 Jan 15, 2023. |
+ | |||
#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 871: | Line 872: | ||
#Ao J, <i>et al.</i> (2015) "Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation." <i>PLoS Genet</i> <b>11</b>(4):e1005118; PMID: [https://pubmed.ncbi.nlm.nih.gov/25835551 25835551]; doi: [https://dx.doi.org/10.1371/journal.pgen.1005118 10.1371/journal.pgen.1005118]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25835551 20]. | #Ao J, <i>et al.</i> (2015) "Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation." <i>PLoS Genet</i> <b>11</b>(4):e1005118; PMID: [https://pubmed.ncbi.nlm.nih.gov/25835551 25835551]; doi: [https://dx.doi.org/10.1371/journal.pgen.1005118 10.1371/journal.pgen.1005118]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25835551 20]. | ||
#Lardi M, <i>et al.</i> (2015) "σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111." <i>Appl Environ Microbiol</i> <b>81</b>(12):4077–89; PMID: [https://pubmed.ncbi.nlm.nih.gov/25841012 25841012]; doi: [https://dx.doi.org/10.1128/AEM.00694-15 10.1128/AEM.00694-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841012 40]. | #Lardi M, <i>et al.</i> (2015) "σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111." <i>Appl Environ Microbiol</i> <b>81</b>(12):4077–89; PMID: [https://pubmed.ncbi.nlm.nih.gov/25841012 25841012]; doi: [https://dx.doi.org/10.1128/AEM.00694-15 10.1128/AEM.00694-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841012 40]. | ||
+ | #Petersen HO, <i>et al.</i> (2015) "A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration." <i>Mol Biol Evol</i> <b>32</b>(8):1928–47; PMID: [https://pubmed.ncbi.nlm.nih.gov/25841488 25841488]; doi: [https://dx.doi.org/10.1093/molbev/msv079 10.1093/molbev/msv079]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841488 198]. | ||
#Piersma SR, <i>et al.</i> (2015) "Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines." <i>J Proteomics</i> <b>127</b>(Pt B):247–58; PMID: [https://pubmed.ncbi.nlm.nih.gov/25841592 25841592]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.03.019 10.1016/j.jprot.2015.03.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841592 31]. | #Piersma SR, <i>et al.</i> (2015) "Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines." <i>J Proteomics</i> <b>127</b>(Pt B):247–58; PMID: [https://pubmed.ncbi.nlm.nih.gov/25841592 25841592]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.03.019 10.1016/j.jprot.2015.03.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841592 31]. | ||
#Krishnan RK, <i>et al.</i> (2015) "Quantitative analysis of the TNF-α-induced phosphoproteome reveals AEG-1/MTDH/LYRIC as an IKKβ substrate." <i>Nat Commun</i> <b>6</b>:6658; PMID: [https://pubmed.ncbi.nlm.nih.gov/25849741 25849741]; doi: [https://dx.doi.org/10.1038/ncomms7658 10.1038/ncomms7658]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25849741 53]. | #Krishnan RK, <i>et al.</i> (2015) "Quantitative analysis of the TNF-α-induced phosphoproteome reveals AEG-1/MTDH/LYRIC as an IKKβ substrate." <i>Nat Commun</i> <b>6</b>:6658; PMID: [https://pubmed.ncbi.nlm.nih.gov/25849741 25849741]; doi: [https://dx.doi.org/10.1038/ncomms7658 10.1038/ncomms7658]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25849741 53]. | ||
Line 2,584: | Line 2,586: | ||
#Buenafe AC, <i>et al.</i> (2022) "Proteomic analysis distinguishes extracellular vesicles produced by cancerous versus healthy pancreatic organoids." <i>Sci Rep</i> <b>12</b>(1):3556; PMID: [https://pubmed.ncbi.nlm.nih.gov/35241737 35241737]; doi: [https://dx.doi.org/10.1038/s41598-022-07451-6 10.1038/s41598-022-07451-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35241737 8]. | #Buenafe AC, <i>et al.</i> (2022) "Proteomic analysis distinguishes extracellular vesicles produced by cancerous versus healthy pancreatic organoids." <i>Sci Rep</i> <b>12</b>(1):3556; PMID: [https://pubmed.ncbi.nlm.nih.gov/35241737 35241737]; doi: [https://dx.doi.org/10.1038/s41598-022-07451-6 10.1038/s41598-022-07451-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35241737 8]. | ||
#McCullough EL, <i>et al.</i> (2022) "The life history of <i>Drosophila</i> sperm involves molecular continuity between male and female reproductive tracts." <i>Proc Natl Acad Sci U S A</i> <b>119</b>(11):e2119899119; PMID: [https://pubmed.ncbi.nlm.nih.gov/35254899 35254899]; doi: [https://dx.doi.org/10.1073/pnas.2119899119 10.1073/pnas.2119899119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35254899 95]. | #McCullough EL, <i>et al.</i> (2022) "The life history of <i>Drosophila</i> sperm involves molecular continuity between male and female reproductive tracts." <i>Proc Natl Acad Sci U S A</i> <b>119</b>(11):e2119899119; PMID: [https://pubmed.ncbi.nlm.nih.gov/35254899 35254899]; doi: [https://dx.doi.org/10.1073/pnas.2119899119 10.1073/pnas.2119899119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35254899 95]. | ||
+ | #May DG, <i>et al.</i> (2022) "A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins." <i>Viruses</i> <b>14</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35337019 35337019]; doi: [https://dx.doi.org/10.3390/v14030611 10.3390/v14030611]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35337019 208]. | ||
#Krumm J, <i>et al.</i> (2022) "High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development." <i>Cell Rep</i> <b>38</b>(13):110604; PMID: [https://pubmed.ncbi.nlm.nih.gov/35354033 35354033]; doi: [https://dx.doi.org/10.1016/j.celrep.2022.110604 10.1016/j.celrep.2022.110604]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35354033 490]. | #Krumm J, <i>et al.</i> (2022) "High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development." <i>Cell Rep</i> <b>38</b>(13):110604; PMID: [https://pubmed.ncbi.nlm.nih.gov/35354033 35354033]; doi: [https://dx.doi.org/10.1016/j.celrep.2022.110604 10.1016/j.celrep.2022.110604]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35354033 490]. | ||
#Croon M, <i>et al.</i> (2022) "FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction." <i>Sci Adv</i> <b>8</b>(14):eabn7105; PMID: [https://pubmed.ncbi.nlm.nih.gov/35385313 35385313]; doi: [https://dx.doi.org/10.1126/sciadv.abn7105 10.1126/sciadv.abn7105]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35385313 71]. | #Croon M, <i>et al.</i> (2022) "FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction." <i>Sci Adv</i> <b>8</b>(14):eabn7105; PMID: [https://pubmed.ncbi.nlm.nih.gov/35385313 35385313]; doi: [https://dx.doi.org/10.1126/sciadv.abn7105 10.1126/sciadv.abn7105]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35385313 71]. | ||
Line 2,596: | Line 2,599: | ||
#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]. | ||
#Crawford RA, <i>et al.</i> (2022) "Cytosolic aspartate aminotransferase moonlights as a ribosome-binding modulator of Gcn2 activity during oxidative stress." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35621265 35621265]; doi: [https://dx.doi.org/10.7554/eLife.73466 10.7554/eLife.73466]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35621265 72]. | #Crawford RA, <i>et al.</i> (2022) "Cytosolic aspartate aminotransferase moonlights as a ribosome-binding modulator of Gcn2 activity during oxidative stress." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35621265 35621265]; doi: [https://dx.doi.org/10.7554/eLife.73466 10.7554/eLife.73466]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35621265 72]. | ||
+ | #Franke K, <i>et al.</i> (2022) "The SCF/KIT axis in human mast cells: Capicua acts as potent KIT repressor and ERK predominates PI3K." <i>Allergy</i> <b>77</b>(11):3337–3349; PMID: [https://pubmed.ncbi.nlm.nih.gov/35652819 35652819]; doi: [https://dx.doi.org/10.1111/all.15396 10.1111/all.15396]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35652819 27]. | ||
#Shkrigunov T, <i>et al.</i> (2022) "Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi." <i>Curr Issues Mol Biol</i> <b>44</b>(5):2069–2088; PMID: [https://pubmed.ncbi.nlm.nih.gov/35678669 35678669]; doi: [https://dx.doi.org/10.3390/cimb44050140 10.3390/cimb44050140]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35678669 43]. | #Shkrigunov T, <i>et al.</i> (2022) "Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi." <i>Curr Issues Mol Biol</i> <b>44</b>(5):2069–2088; PMID: [https://pubmed.ncbi.nlm.nih.gov/35678669 35678669]; doi: [https://dx.doi.org/10.3390/cimb44050140 10.3390/cimb44050140]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35678669 43]. | ||
#Voß H, <i>et al.</i> (2022) "Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine." <i>Int J Mol Sci</i> <b>23</b>(11):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35682811 35682811]; doi: [https://dx.doi.org/10.3390/ijms23116132 10.3390/ijms23116132]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35682811 24]. | #Voß H, <i>et al.</i> (2022) "Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine." <i>Int J Mol Sci</i> <b>23</b>(11):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35682811 35682811]; doi: [https://dx.doi.org/10.3390/ijms23116132 10.3390/ijms23116132]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35682811 24]. | ||
#Schneider MF, <i>et al.</i> (2022) "LncRNA <i>RUS</i> shapes the gene expression program towards neurogenesis." <i>Life Sci Alliance</i> <b>5</b>(10):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35688487 35688487]; doi: [https://dx.doi.org/10.26508/lsa.202201504 10.26508/lsa.202201504]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35688487 10]. | #Schneider MF, <i>et al.</i> (2022) "LncRNA <i>RUS</i> shapes the gene expression program towards neurogenesis." <i>Life Sci Alliance</i> <b>5</b>(10):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35688487 35688487]; doi: [https://dx.doi.org/10.26508/lsa.202201504 10.26508/lsa.202201504]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35688487 10]. | ||
#Wu C, <i>et al.</i> (2022) "Efficient Detection of the Alternative Spliced Human Proteome Using Translatome Sequencing." <i>Front Mol Biosci</i> <b>9</b>:895746; PMID: [https://pubmed.ncbi.nlm.nih.gov/35720116 35720116]; doi: [https://dx.doi.org/10.3389/fmolb.2022.895746 10.3389/fmolb.2022.895746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35720116 1]. | #Wu C, <i>et al.</i> (2022) "Efficient Detection of the Alternative Spliced Human Proteome Using Translatome Sequencing." <i>Front Mol Biosci</i> <b>9</b>:895746; PMID: [https://pubmed.ncbi.nlm.nih.gov/35720116 35720116]; doi: [https://dx.doi.org/10.3389/fmolb.2022.895746 10.3389/fmolb.2022.895746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35720116 1]. | ||
+ | #Guo J, <i>et al.</i> (2022) "Proteomic Analysis of Human Milk Reveals Nutritional and Immune Benefits in the Colostrum from Mothers with COVID-19." <i>Nutrients</i> <b>14</b>(12):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35745243 35745243]; doi: [https://dx.doi.org/10.3390/nu14122513 10.3390/nu14122513]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35745243 32]. | ||
#Su PR, <i>et al.</i> (2022) "Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics." <i>Cell Rep Methods</i> <b>2</b>(6):100237; PMID: [https://pubmed.ncbi.nlm.nih.gov/35784653 35784653]; doi: [https://dx.doi.org/10.1016/j.crmeth.2022.100237 10.1016/j.crmeth.2022.100237]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35784653 34]. | #Su PR, <i>et al.</i> (2022) "Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics." <i>Cell Rep Methods</i> <b>2</b>(6):100237; PMID: [https://pubmed.ncbi.nlm.nih.gov/35784653 35784653]; doi: [https://dx.doi.org/10.1016/j.crmeth.2022.100237 10.1016/j.crmeth.2022.100237]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35784653 34]. | ||
#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]. | ||
+ | #Val-Blasco A, <i>et al.</i> (2022) "Specialized Proresolving Mediators Protect Against Experimental Autoimmune Myocarditis by Modulating Ca(2+) Handling and NRF2 Activation." <i>JACC Basic Transl Sci</i> <b>7</b>(6):544–560; PMID: [https://pubmed.ncbi.nlm.nih.gov/35818504 35818504]; doi: [https://dx.doi.org/10.1016/j.jacbts.2022.01.009 10.1016/j.jacbts.2022.01.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35818504 6]. | ||
#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]. | #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]. | ||
Line 2,619: | Line 2,625: | ||
#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 34]. | #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 34]. | ||
#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]. | #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]. | ||
+ | #Yammine M, <i>et al.</i> (2022) "Reliable Approach for Pure Yeast Cell Wall Protein Isolation from Saccharomyces cerevisiae Yeast Cells." <i>ACS Omega</i> <b>7</b>(34):29702–29713; PMID: [https://pubmed.ncbi.nlm.nih.gov/36061670 36061670]; doi: [https://dx.doi.org/10.1021/acsomega.2c02176 10.1021/acsomega.2c02176]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36061670 45]. | ||
#Singh SS, <i>et al.</i> (2022) "Multi-omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress." <i>Proteomics</i> <b></b>:e2200148; PMID: [https://pubmed.ncbi.nlm.nih.gov/36066285 36066285]; doi: [https://dx.doi.org/10.1002/pmic.202200148 10.1002/pmic.202200148]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36066285 9]. | #Singh SS, <i>et al.</i> (2022) "Multi-omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress." <i>Proteomics</i> <b></b>:e2200148; PMID: [https://pubmed.ncbi.nlm.nih.gov/36066285 36066285]; doi: [https://dx.doi.org/10.1002/pmic.202200148 10.1002/pmic.202200148]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36066285 9]. | ||
#Pechincha C, <i>et al.</i> (2022) "Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins." <i>Science</i> <b>378</b>(6615):eabn5637; PMID: [https://pubmed.ncbi.nlm.nih.gov/36074822 36074822]; doi: [https://dx.doi.org/10.1126/science.abn5637 10.1126/science.abn5637]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36074822 29]. | #Pechincha C, <i>et al.</i> (2022) "Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins." <i>Science</i> <b>378</b>(6615):eabn5637; PMID: [https://pubmed.ncbi.nlm.nih.gov/36074822 36074822]; doi: [https://dx.doi.org/10.1126/science.abn5637 10.1126/science.abn5637]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36074822 29]. | ||
Line 2,626: | Line 2,633: | ||
#Arora A, <i>et al.</i> (2022) "High-throughput identification of RNA localization elements in neuronal cells." <i>Nucleic Acids Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36107770 36107770]; doi: [https://dx.doi.org/10.1093/nar/gkac763 10.1093/nar/gkac763]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36107770 24]. | #Arora A, <i>et al.</i> (2022) "High-throughput identification of RNA localization elements in neuronal cells." <i>Nucleic Acids Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36107770 36107770]; doi: [https://dx.doi.org/10.1093/nar/gkac763 10.1093/nar/gkac763]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36107770 24]. | ||
#Sapao P, <i>et al.</i> (2022) "Reduced SPAG17 expression in systemic sclerosis triggers myofibroblast transition and drives fibrosis." <i>J Invest Dermatol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36116512 36116512]; doi: [https://dx.doi.org/10.1016/j.jid.2022.08.052 10.1016/j.jid.2022.08.052]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36116512 15]. | #Sapao P, <i>et al.</i> (2022) "Reduced SPAG17 expression in systemic sclerosis triggers myofibroblast transition and drives fibrosis." <i>J Invest Dermatol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36116512 36116512]; doi: [https://dx.doi.org/10.1016/j.jid.2022.08.052 10.1016/j.jid.2022.08.052]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36116512 15]. | ||
+ | #de Melo TC, <i>et al.</i> (2022) "Proteomic Analysis Identifies Molecular Players and Biological Processes Specific to SARS-CoV-2 Exposure in Endothelial Cells." <i>Int J Mol Sci</i> <b>23</b>(18):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36142365 36142365]; doi: [https://dx.doi.org/10.3390/ijms231810452 10.3390/ijms231810452]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36142365 22]. | ||
#Monks J, <i>et al.</i> (2022) "Perilipin-2 promotes lipid droplet-plasma membrane interactions that facilitate apocrine lipid secretion in secretory epithelial cells of the mouse mammary gland." <i>Front Cell Dev Biol</i> <b>10</b>:958566; PMID: [https://pubmed.ncbi.nlm.nih.gov/36158190 36158190]; doi: [https://dx.doi.org/10.3389/fcell.2022.958566 10.3389/fcell.2022.958566]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36158190 10]. | #Monks J, <i>et al.</i> (2022) "Perilipin-2 promotes lipid droplet-plasma membrane interactions that facilitate apocrine lipid secretion in secretory epithelial cells of the mouse mammary gland." <i>Front Cell Dev Biol</i> <b>10</b>:958566; PMID: [https://pubmed.ncbi.nlm.nih.gov/36158190 36158190]; doi: [https://dx.doi.org/10.3389/fcell.2022.958566 10.3389/fcell.2022.958566]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36158190 10]. | ||
#Deng O, <i>et al.</i> (2022) "Integrated proteomics identifies PARP inhibitor-induced pro-survival signaling changes as potential vulnerabilities in ovarian cancer." <i>J Biol Chem</i> <b></b>:102550; PMID: [https://pubmed.ncbi.nlm.nih.gov/36183837 36183837]; doi: [https://dx.doi.org/10.1016/j.jbc.2022.102550 10.1016/j.jbc.2022.102550]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36183837 41]. | #Deng O, <i>et al.</i> (2022) "Integrated proteomics identifies PARP inhibitor-induced pro-survival signaling changes as potential vulnerabilities in ovarian cancer." <i>J Biol Chem</i> <b></b>:102550; PMID: [https://pubmed.ncbi.nlm.nih.gov/36183837 36183837]; doi: [https://dx.doi.org/10.1016/j.jbc.2022.102550 10.1016/j.jbc.2022.102550]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36183837 41]. | ||
#Ventura PMO, <i>et al.</i> (2022) "Concomitant deletion of Ptpn6 and Ptpn11 in T cells fails to improve anticancer responses." <i>EMBO Rep</i> <b></b>:e55399; PMID: [https://pubmed.ncbi.nlm.nih.gov/36194675 36194675]; doi: [https://dx.doi.org/10.15252/embr.202255399 10.15252/embr.202255399]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36194675 6]. | #Ventura PMO, <i>et al.</i> (2022) "Concomitant deletion of Ptpn6 and Ptpn11 in T cells fails to improve anticancer responses." <i>EMBO Rep</i> <b></b>:e55399; PMID: [https://pubmed.ncbi.nlm.nih.gov/36194675 36194675]; doi: [https://dx.doi.org/10.15252/embr.202255399 10.15252/embr.202255399]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36194675 6]. | ||
#Bernhardt M, <i>et al.</i> (2022) "Extending the Mass Spectrometry-Detectable Landscape of MHC Peptides by Use of Restricted Access Material." <i>Anal Chem</i> <b>94</b>(41):14214–14222; PMID: [https://pubmed.ncbi.nlm.nih.gov/36194871 36194871]; doi: [https://dx.doi.org/10.1021/acs.analchem.2c02198 10.1021/acs.analchem.2c02198]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36194871 76]. | #Bernhardt M, <i>et al.</i> (2022) "Extending the Mass Spectrometry-Detectable Landscape of MHC Peptides by Use of Restricted Access Material." <i>Anal Chem</i> <b>94</b>(41):14214–14222; PMID: [https://pubmed.ncbi.nlm.nih.gov/36194871 36194871]; doi: [https://dx.doi.org/10.1021/acs.analchem.2c02198 10.1021/acs.analchem.2c02198]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36194871 76]. | ||
+ | #Chavkin NW, <i>et al.</i> (2022) "Endothelial cell cycle state determines propensity for arterial-venous fate." <i>Nat Commun</i> <b>13</b>(1):5891; PMID: [https://pubmed.ncbi.nlm.nih.gov/36202789 36202789]; doi: [https://dx.doi.org/10.1038/s41467-022-33324-7 10.1038/s41467-022-33324-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36202789 12]. | ||
#Léger T, <i>et al.</i> (2022) "Fate and PPARγ and STATs-driven effects of the mitochondrial complex I inhibitor tebufenpyrad in liver cells revealed with multi-omics." <i>J Hazard Mater</i> <b>442</b>:130083; PMID: [https://pubmed.ncbi.nlm.nih.gov/36206710 36206710]; doi: [https://dx.doi.org/10.1016/j.jhazmat.2022.130083 10.1016/j.jhazmat.2022.130083]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36206710 96]. | #Léger T, <i>et al.</i> (2022) "Fate and PPARγ and STATs-driven effects of the mitochondrial complex I inhibitor tebufenpyrad in liver cells revealed with multi-omics." <i>J Hazard Mater</i> <b>442</b>:130083; PMID: [https://pubmed.ncbi.nlm.nih.gov/36206710 36206710]; doi: [https://dx.doi.org/10.1016/j.jhazmat.2022.130083 10.1016/j.jhazmat.2022.130083]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36206710 96]. | ||
- | #Noborn F, <i>et al.</i> (2022) "Subtyping of cardiac amyloidosis by mass spectrometry-based proteomics of endomyocardial biopsies." <i>Amyloid</i> <b></b>:1–13; PMID: [https://pubmed.ncbi.nlm.nih.gov/36209425 36209425]; doi: [https://dx.doi.org/10.1080/13506129.2022.2127088 10.1080/13506129.2022.2127088]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36209425 | + | #Noborn F, <i>et al.</i> (2022) "Subtyping of cardiac amyloidosis by mass spectrometry-based proteomics of endomyocardial biopsies." <i>Amyloid</i> <b></b>:1–13; PMID: [https://pubmed.ncbi.nlm.nih.gov/36209425 36209425]; doi: [https://dx.doi.org/10.1080/13506129.2022.2127088 10.1080/13506129.2022.2127088]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36209425 343]. |
#Vilallongue N, <i>et al.</i> (2022) "Guidance landscapes unveiled by quantitative proteomics to control reinnervation in adult visual system." <i>Nat Commun</i> <b>13</b>(1):6040; PMID: [https://pubmed.ncbi.nlm.nih.gov/36229455 36229455]; doi: [https://dx.doi.org/10.1038/s41467-022-33799-4 10.1038/s41467-022-33799-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36229455 40]. | #Vilallongue N, <i>et al.</i> (2022) "Guidance landscapes unveiled by quantitative proteomics to control reinnervation in adult visual system." <i>Nat Commun</i> <b>13</b>(1):6040; PMID: [https://pubmed.ncbi.nlm.nih.gov/36229455 36229455]; doi: [https://dx.doi.org/10.1038/s41467-022-33799-4 10.1038/s41467-022-33799-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36229455 40]. | ||
#Bracht T, <i>et al.</i> (2022) "Plasma Proteomics Enable Differentiation of Lung Adenocarcinoma from Chronic Obstructive Pulmonary Disease (COPD)." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36232544 36232544]; doi: [https://dx.doi.org/10.3390/ijms231911242 10.3390/ijms231911242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36232544 171]. | #Bracht T, <i>et al.</i> (2022) "Plasma Proteomics Enable Differentiation of Lung Adenocarcinoma from Chronic Obstructive Pulmonary Disease (COPD)." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36232544 36232544]; doi: [https://dx.doi.org/10.3390/ijms231911242 10.3390/ijms231911242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36232544 171]. | ||
#Elsnicova B, <i>et al.</i> (2022) "Desmin Knock-Out Cardiomyopathy: A Heart on the Verge of Metabolic Crisis." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36233322 36233322]; doi: [https://dx.doi.org/10.3390/ijms231912020 10.3390/ijms231912020]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36233322 10]. | #Elsnicova B, <i>et al.</i> (2022) "Desmin Knock-Out Cardiomyopathy: A Heart on the Verge of Metabolic Crisis." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36233322 36233322]; doi: [https://dx.doi.org/10.3390/ijms231912020 10.3390/ijms231912020]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36233322 10]. | ||
+ | #Kalpongnukul N, <i>et al.</i> (2022) "Phosphoproteomic Analysis Defines BABAM1 as mTORC2 Downstream Effector Promoting DNA Damage Response in Glioblastoma Cells." <i>J Proteome Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36315652 36315652]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00240 10.1021/acs.jproteome.2c00240]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36315652 400]. | ||
+ | #Busso-Lopes AF, <i>et al.</i> (2022) "Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer." <i>Nat Commun</i> <b>13</b>(1):6725; PMID: [https://pubmed.ncbi.nlm.nih.gov/36344512 36344512]; doi: [https://dx.doi.org/10.1038/s41467-022-34407-1 10.1038/s41467-022-34407-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36344512 140]. | ||
+ | #Jang Y, <i>et al.</i> (2022) "Mass spectrometry-based proteomics analysis of human globus pallidus from progressive supranuclear palsy patients discovers multiple disease pathways." <i>Clin Transl Med</i> <b>12</b>(11):e1076; PMID: [https://pubmed.ncbi.nlm.nih.gov/36354133 36354133]; doi: [https://dx.doi.org/10.1002/ctm2.1076 10.1002/ctm2.1076]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36354133 6]. | ||
+ | #Jang Y, <i>et al.</i> (2022) "Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease." <i>Mol Cell Proteomics</i> <b>22</b>(1):100452; PMID: [https://pubmed.ncbi.nlm.nih.gov/36423813 36423813]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100452 10.1016/j.mcpro.2022.100452]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36423813 5]. | ||
+ | #Banerjee A, <i>et al.</i> (2022) "The first Pituitary Proteome Landscape from matched anterior and posterior lobes for a better understanding of the Pituitary Gland." <i>Mol Cell Proteomics</i> <b></b>:100478; PMID: [https://pubmed.ncbi.nlm.nih.gov/36470533 36470533]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100478 10.1016/j.mcpro.2022.100478]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36470533 10]. | ||
+ | #Mitchell DC, <i>et al.</i> (2023) "A proteome-wide atlas of drug mechanism of action." <i>Nat Biotechnol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36593396 36593396]; doi: [https://dx.doi.org/10.1038/s41587-022-01539-0 10.1038/s41587-022-01539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36593396 342]. |
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 Jan 15, 2023.