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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 July 31, 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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#Bisson N, <i>et al.</i> (2011) "Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor." <i>Nat Biotechnol</i> <b>29</b>(7):653–8; PMID: [https://pubmed.ncbi.nlm.nih.gov/21706016 21706016]; doi: [https://dx.doi.org/10.1038/nbt.1905 10.1038/nbt.1905]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21706016 5]. | #Bisson N, <i>et al.</i> (2011) "Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor." <i>Nat Biotechnol</i> <b>29</b>(7):653–8; PMID: [https://pubmed.ncbi.nlm.nih.gov/21706016 21706016]; doi: [https://dx.doi.org/10.1038/nbt.1905 10.1038/nbt.1905]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21706016 5]. | ||
#Kettenbach AN, <i>et al.</i> (2011) "Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells." <i>Sci Signal</i> <b>4</b>(179):rs5; PMID: [https://pubmed.ncbi.nlm.nih.gov/21712546 21712546]; doi: [https://dx.doi.org/10.1126/scisignal.2001497 10.1126/scisignal.2001497]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21712546 100]. | #Kettenbach AN, <i>et al.</i> (2011) "Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells." <i>Sci Signal</i> <b>4</b>(179):rs5; PMID: [https://pubmed.ncbi.nlm.nih.gov/21712546 21712546]; doi: [https://dx.doi.org/10.1126/scisignal.2001497 10.1126/scisignal.2001497]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21712546 100]. | ||
+ | #Liao Y, <i>et al.</i> (2011) "Proteomic characterization of human milk fat globule membrane proteins during a 12 month lactation period." <i>J Proteome Res</i> <b>10</b>(8):3530–41; PMID: [https://pubmed.ncbi.nlm.nih.gov/21714549 21714549]; doi: [https://dx.doi.org/10.1021/pr200149t 10.1021/pr200149t]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21714549 90]. | ||
#Bradel-Tretheway BG, <i>et al.</i> (2011) "Comprehensive proteomic analysis of influenza virus polymerase complex reveals a novel association with mitochondrial proteins and RNA polymerase accessory factors." <i>J Virol</i> <b>85</b>(17):8569–81; PMID: [https://pubmed.ncbi.nlm.nih.gov/21715506 21715506]; doi: [https://dx.doi.org/10.1128/JVI.00496-11 10.1128/JVI.00496-11]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21715506 22]. | #Bradel-Tretheway BG, <i>et al.</i> (2011) "Comprehensive proteomic analysis of influenza virus polymerase complex reveals a novel association with mitochondrial proteins and RNA polymerase accessory factors." <i>J Virol</i> <b>85</b>(17):8569–81; PMID: [https://pubmed.ncbi.nlm.nih.gov/21715506 21715506]; doi: [https://dx.doi.org/10.1128/JVI.00496-11 10.1128/JVI.00496-11]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21715506 22]. | ||
#Freschi L, <i>et al.</i> (2011) "Phosphorylation network rewiring by gene duplication." <i>Mol Syst Biol</i> <b>7</b>:504; PMID: [https://pubmed.ncbi.nlm.nih.gov/21734643 21734643]; doi: [https://dx.doi.org/10.1038/msb.2011.43 10.1038/msb.2011.43]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21734643 2]. | #Freschi L, <i>et al.</i> (2011) "Phosphorylation network rewiring by gene duplication." <i>Mol Syst Biol</i> <b>7</b>:504; PMID: [https://pubmed.ncbi.nlm.nih.gov/21734643 21734643]; doi: [https://dx.doi.org/10.1038/msb.2011.43 10.1038/msb.2011.43]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21734643 2]. | ||
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#Sghaier H, <i>et al.</i> (2016) "Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes." <i>ISME J</i> <b>10</b>(1):21–9; PMID: [https://pubmed.ncbi.nlm.nih.gov/26125681 26125681]; doi: [https://dx.doi.org/10.1038/ismej.2015.108 10.1038/ismej.2015.108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26125681 9]. | #Sghaier H, <i>et al.</i> (2016) "Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes." <i>ISME J</i> <b>10</b>(1):21–9; PMID: [https://pubmed.ncbi.nlm.nih.gov/26125681 26125681]; doi: [https://dx.doi.org/10.1038/ismej.2015.108 10.1038/ismej.2015.108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26125681 9]. | ||
#Carapito C, <i>et al.</i> (2015) "Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14." <i>J Proteome Res</i> <b>14</b>(9):3621–34; PMID: [https://pubmed.ncbi.nlm.nih.gov/26132440 26132440]; doi: [https://dx.doi.org/10.1021/pr5010345 10.1021/pr5010345]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26132440 58]. | #Carapito C, <i>et al.</i> (2015) "Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14." <i>J Proteome Res</i> <b>14</b>(9):3621–34; PMID: [https://pubmed.ncbi.nlm.nih.gov/26132440 26132440]; doi: [https://dx.doi.org/10.1021/pr5010345 10.1021/pr5010345]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26132440 58]. | ||
+ | #Walz S, <i>et al.</i> (2015) "The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy." <i>Blood</i> <b>126</b>(10):1203–13; PMID: [https://pubmed.ncbi.nlm.nih.gov/26138685 26138685]; doi: [https://dx.doi.org/10.1182/blood-2015-04-640532 10.1182/blood-2015-04-640532]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26138685 177]. | ||
#Dislich B, <i>et al.</i> (2015) "Label-free Quantitative Proteomics of Mouse Cerebrospinal Fluid Detects β-Site APP Cleaving Enzyme (BACE1) Protease Substrates In Vivo." <i>Mol Cell Proteomics</i> <b>14</b>(10):2550–63; PMID: [https://pubmed.ncbi.nlm.nih.gov/26139848 26139848]; doi: [https://dx.doi.org/10.1074/mcp.M114.041533 10.1074/mcp.M114.041533]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26139848 26]. | #Dislich B, <i>et al.</i> (2015) "Label-free Quantitative Proteomics of Mouse Cerebrospinal Fluid Detects β-Site APP Cleaving Enzyme (BACE1) Protease Substrates In Vivo." <i>Mol Cell Proteomics</i> <b>14</b>(10):2550–63; PMID: [https://pubmed.ncbi.nlm.nih.gov/26139848 26139848]; doi: [https://dx.doi.org/10.1074/mcp.M114.041533 10.1074/mcp.M114.041533]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26139848 26]. | ||
#Swaney DL, <i>et al.</i> (2015) "Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover." <i>EMBO Rep</i> <b>16</b>(9):1131–44; PMID: [https://pubmed.ncbi.nlm.nih.gov/26142280 26142280]; doi: [https://dx.doi.org/10.15252/embr.201540298 10.15252/embr.201540298]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26142280 56]. | #Swaney DL, <i>et al.</i> (2015) "Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover." <i>EMBO Rep</i> <b>16</b>(9):1131–44; PMID: [https://pubmed.ncbi.nlm.nih.gov/26142280 26142280]; doi: [https://dx.doi.org/10.15252/embr.201540298 10.15252/embr.201540298]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26142280 56]. | ||
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#Lee-Law PY, <i>et al.</i> (2021) "Targeting UBC9-mediated protein hyper-SUMOylation in cystic cholangiocytes halts polycystic liver disease in experimental models." <i>J Hepatol</i> <b>74</b>(2):394–406; PMID: [https://pubmed.ncbi.nlm.nih.gov/32950589 32950589]; doi: [https://dx.doi.org/10.1016/j.jhep.2020.09.010 10.1016/j.jhep.2020.09.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32950589 49]. | #Lee-Law PY, <i>et al.</i> (2021) "Targeting UBC9-mediated protein hyper-SUMOylation in cystic cholangiocytes halts polycystic liver disease in experimental models." <i>J Hepatol</i> <b>74</b>(2):394–406; PMID: [https://pubmed.ncbi.nlm.nih.gov/32950589 32950589]; doi: [https://dx.doi.org/10.1016/j.jhep.2020.09.010 10.1016/j.jhep.2020.09.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32950589 49]. | ||
#Liu JJ, <i>et al.</i> (2020) "Pharmacological and phosphoproteomic approaches to roles of protein kinase C in kappa opioid receptor-mediated effects in mice." <i>Neuropharmacology</i> <b>181</b>:108324; PMID: [https://pubmed.ncbi.nlm.nih.gov/32976891 32976891]; doi: [https://dx.doi.org/10.1016/j.neuropharm.2020.108324 10.1016/j.neuropharm.2020.108324]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32976891 67]. | #Liu JJ, <i>et al.</i> (2020) "Pharmacological and phosphoproteomic approaches to roles of protein kinase C in kappa opioid receptor-mediated effects in mice." <i>Neuropharmacology</i> <b>181</b>:108324; PMID: [https://pubmed.ncbi.nlm.nih.gov/32976891 32976891]; doi: [https://dx.doi.org/10.1016/j.neuropharm.2020.108324 10.1016/j.neuropharm.2020.108324]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32976891 67]. | ||
+ | #Marino F, <i>et al.</i> (2020) "Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference." <i>Front Immunol</i> <b>11</b>:1981; PMID: [https://pubmed.ncbi.nlm.nih.gov/32983136 32983136]; doi: [https://dx.doi.org/10.3389/fimmu.2020.01981 10.3389/fimmu.2020.01981]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32983136 221]. | ||
#Schumacher N, <i>et al.</i> (2021) "Cell-autonomous hepatocyte-specific GP130 signaling is sufficient to trigger a robust innate immune response in mice." <i>J Hepatol</i> <b>74</b>(2):407–418; PMID: [https://pubmed.ncbi.nlm.nih.gov/32987028 32987028]; doi: [https://dx.doi.org/10.1016/j.jhep.2020.09.021 10.1016/j.jhep.2020.09.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32987028 1]. | #Schumacher N, <i>et al.</i> (2021) "Cell-autonomous hepatocyte-specific GP130 signaling is sufficient to trigger a robust innate immune response in mice." <i>J Hepatol</i> <b>74</b>(2):407–418; PMID: [https://pubmed.ncbi.nlm.nih.gov/32987028 32987028]; doi: [https://dx.doi.org/10.1016/j.jhep.2020.09.021 10.1016/j.jhep.2020.09.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32987028 1]. | ||
#Adhikari B, <i>et al.</i> (2020) "PROTAC-mediated degradation reveals a non-catalytic function of AURORA-A kinase." <i>Nat Chem Biol</i> <b>16</b>(11):1179–1188; PMID: [https://pubmed.ncbi.nlm.nih.gov/32989298 32989298]; doi: [https://dx.doi.org/10.1038/s41589-020-00652-y 10.1038/s41589-020-00652-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32989298 93]. | #Adhikari B, <i>et al.</i> (2020) "PROTAC-mediated degradation reveals a non-catalytic function of AURORA-A kinase." <i>Nat Chem Biol</i> <b>16</b>(11):1179–1188; PMID: [https://pubmed.ncbi.nlm.nih.gov/32989298 32989298]; doi: [https://dx.doi.org/10.1038/s41589-020-00652-y 10.1038/s41589-020-00652-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32989298 93]. | ||
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#Chen L, <i>et al.</i> (2021) "Combined Transcriptome and Proteome Profiling for Role of pfEMP1 in Antimalarial Mechanism of Action of Dihydroartemisinin." <i>Microbiol Spectr</i> <b>9</b>(3):e0127821; PMID: [https://pubmed.ncbi.nlm.nih.gov/34908430 34908430]; doi: [https://dx.doi.org/10.1128/Spectrum.01278-21 10.1128/Spectrum.01278-21]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34908430 1]. | #Chen L, <i>et al.</i> (2021) "Combined Transcriptome and Proteome Profiling for Role of pfEMP1 in Antimalarial Mechanism of Action of Dihydroartemisinin." <i>Microbiol Spectr</i> <b>9</b>(3):e0127821; PMID: [https://pubmed.ncbi.nlm.nih.gov/34908430 34908430]; doi: [https://dx.doi.org/10.1128/Spectrum.01278-21 10.1128/Spectrum.01278-21]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34908430 1]. | ||
#Wang Q, <i>et al.</i> (2021) "Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) is upregulated in breast epithelial-mesenchymal transition and responds to oxidative stress." <i>Mol Cell Proteomics</i> <b></b>:100185; PMID: [https://pubmed.ncbi.nlm.nih.gov/34923141 34923141]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100185 10.1016/j.mcpro.2021.100185]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34923141 32]. | #Wang Q, <i>et al.</i> (2021) "Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) is upregulated in breast epithelial-mesenchymal transition and responds to oxidative stress." <i>Mol Cell Proteomics</i> <b></b>:100185; PMID: [https://pubmed.ncbi.nlm.nih.gov/34923141 34923141]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100185 10.1016/j.mcpro.2021.100185]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34923141 32]. | ||
+ | #Koehler S, <i>et al.</i> (2022) "Scaffold polarity proteins Par3A and Par3B share redundant functions while Par3B acts independent of atypical protein kinase C/Par6 in podocytes to maintain the kidney filtration barrier." <i>Kidney Int</i> <b>101</b>(4):733–751; PMID: [https://pubmed.ncbi.nlm.nih.gov/34929254 34929254]; doi: [https://dx.doi.org/10.1016/j.kint.2021.11.030 10.1016/j.kint.2021.11.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34929254 41]. | ||
#Thorne LG, <i>et al.</i> (2021) "Evolution of enhanced innate immune evasion by SARS-CoV-2." <i>Nature</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/34942634 34942634]; doi: [https://dx.doi.org/10.1038/s41586-021-04352-y 10.1038/s41586-021-04352-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34942634 16]. | #Thorne LG, <i>et al.</i> (2021) "Evolution of enhanced innate immune evasion by SARS-CoV-2." <i>Nature</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/34942634 34942634]; doi: [https://dx.doi.org/10.1038/s41586-021-04352-y 10.1038/s41586-021-04352-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34942634 16]. | ||
#Key J, <i>et al.</i> (2021) "Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX with Its Interacting Nucleoid Proteins, and of mtDNA." <i>Cells</i> <b>10</b>(12):; PMID: [https://pubmed.ncbi.nlm.nih.gov/34943861 34943861]; doi: [https://dx.doi.org/10.3390/cells10123354 10.3390/cells10123354]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34943861 13]. | #Key J, <i>et al.</i> (2021) "Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX with Its Interacting Nucleoid Proteins, and of mtDNA." <i>Cells</i> <b>10</b>(12):; PMID: [https://pubmed.ncbi.nlm.nih.gov/34943861 34943861]; doi: [https://dx.doi.org/10.3390/cells10123354 10.3390/cells10123354]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34943861 13]. | ||
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#Perivolidi VI, <i>et al.</i> (2022) "Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG." <i>J Proteome Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/34983179 34983179]; doi: [https://dx.doi.org/10.1021/acs.jproteome.1c00728 10.1021/acs.jproteome.1c00728]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34983179 24]. | #Perivolidi VI, <i>et al.</i> (2022) "Proteomic Identification of the SLC25A46 Interactome in Transgenic Mice Expressing SLC25A46-FLAG." <i>J Proteome Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/34983179 34983179]; doi: [https://dx.doi.org/10.1021/acs.jproteome.1c00728 10.1021/acs.jproteome.1c00728]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34983179 24]. | ||
#Zille M, <i>et al.</i> (2022) "Hemin-Induced Death Models Hemorrhagic Stroke and Is a Variant of Classical Neuronal Ferroptosis." <i>J Neurosci</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/34987108 34987108]; doi: [https://dx.doi.org/10.1523/JNEUROSCI.0923-20.2021 10.1523/JNEUROSCI.0923-20.2021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34987108 28]. | #Zille M, <i>et al.</i> (2022) "Hemin-Induced Death Models Hemorrhagic Stroke and Is a Variant of Classical Neuronal Ferroptosis." <i>J Neurosci</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/34987108 34987108]; doi: [https://dx.doi.org/10.1523/JNEUROSCI.0923-20.2021 10.1523/JNEUROSCI.0923-20.2021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34987108 28]. | ||
+ | #Tan C, <i>et al.</i> (2021) "Alterations of Asymmetric Dimethylarginine (ADMA)-Containing Protein Profiles Associated with Chronic Pancreatitis Pathogenesis." <i>J Inflamm Res</i> <b>14</b>:7381–7392; PMID: [https://pubmed.ncbi.nlm.nih.gov/34992424 34992424]; doi: [https://dx.doi.org/10.2147/JIR.S346575 10.2147/JIR.S346575]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34992424 12]. | ||
#Buks R, <i>et al.</i> (2021) "Altered Ca<sup>2+</sup> Homeostasis in Red Blood Cells of Polycythemia Vera Patients Following Disturbed Organelle Sorting during Terminal Erythropoiesis." <i>Cells</i> <b>11</b>(1):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35011611 35011611]; doi: [https://dx.doi.org/10.3390/cells11010049 10.3390/cells11010049]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35011611 23]. | #Buks R, <i>et al.</i> (2021) "Altered Ca<sup>2+</sup> Homeostasis in Red Blood Cells of Polycythemia Vera Patients Following Disturbed Organelle Sorting during Terminal Erythropoiesis." <i>Cells</i> <b>11</b>(1):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35011611 35011611]; doi: [https://dx.doi.org/10.3390/cells11010049 10.3390/cells11010049]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35011611 23]. | ||
#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]. | ||
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#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]. | ||
+ | #Ahmed S, <i>et al.</i> (2022) "Urine Proteomics for Noninvasive Monitoring of Biomarkers in Bronchopulmonary Dysplasia." <i>Neonatology</i> <b>119</b>(2):193–203; PMID: [https://pubmed.ncbi.nlm.nih.gov/35073553 35073553]; doi: [https://dx.doi.org/10.1159/000520680 10.1159/000520680]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35073553 42]. | ||
#Ali N, <i>et al.</i> (2022) "Proteomics profiling of human synovial fluid suggests increased protein interplay in early-osteoarthritis (OA) that is lost in late-stage OA." <i>Mol Cell Proteomics</i> <b></b>:100200; PMID: [https://pubmed.ncbi.nlm.nih.gov/35074580 35074580]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100200 10.1016/j.mcpro.2022.100200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35074580 61]. | #Ali N, <i>et al.</i> (2022) "Proteomics profiling of human synovial fluid suggests increased protein interplay in early-osteoarthritis (OA) that is lost in late-stage OA." <i>Mol Cell Proteomics</i> <b></b>:100200; PMID: [https://pubmed.ncbi.nlm.nih.gov/35074580 35074580]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100200 10.1016/j.mcpro.2022.100200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35074580 61]. | ||
#Garcia-Marques F, <i>et al.</i> (2022) "Protein signatures to distinguish aggressive from indolent prostate cancer." <i>Prostate</i> <b>82</b>(5):605–616; PMID: [https://pubmed.ncbi.nlm.nih.gov/35098564 35098564]; doi: [https://dx.doi.org/10.1002/pros.24307 10.1002/pros.24307]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35098564 132]. | #Garcia-Marques F, <i>et al.</i> (2022) "Protein signatures to distinguish aggressive from indolent prostate cancer." <i>Prostate</i> <b>82</b>(5):605–616; PMID: [https://pubmed.ncbi.nlm.nih.gov/35098564 35098564]; doi: [https://dx.doi.org/10.1002/pros.24307 10.1002/pros.24307]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35098564 132]. | ||
Line 2,573: | Line 2,579: | ||
#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]. | ||
#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]. | ||
#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]. | ||
+ | #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]. | ||
+ | #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]. | ||
+ | #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]. | ||
+ | #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]. | ||
+ | #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]. | ||
+ | #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]. | ||
+ | #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]. | ||
+ | #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]. |
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 July 31, 2022.