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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 May | + | 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 May 15, 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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#Kelley RC, <i>et al.</i> (2018) "Advanced aging causes diaphragm functional abnormalities, global proteome remodeling, and loss of mitochondrial cysteine redox flexibility in mice." <i>Exp Gerontol</i> <b>103</b>:69–79; PMID: [https://pubmed.ncbi.nlm.nih.gov/29289553 29289553]; doi: [https://dx.doi.org/10.1016/j.exger.2017.12.017 10.1016/j.exger.2017.12.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29289553 24]. | #Kelley RC, <i>et al.</i> (2018) "Advanced aging causes diaphragm functional abnormalities, global proteome remodeling, and loss of mitochondrial cysteine redox flexibility in mice." <i>Exp Gerontol</i> <b>103</b>:69–79; PMID: [https://pubmed.ncbi.nlm.nih.gov/29289553 29289553]; doi: [https://dx.doi.org/10.1016/j.exger.2017.12.017 10.1016/j.exger.2017.12.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29289553 24]. | ||
#Behr M, <i>et al.</i> (2018) "Insights into the molecular regulation of monolignol-derived product biosynthesis in the growing hemp hypocotyl." <i>BMC Plant Biol</i> <b>18</b>(1):1; PMID: [https://pubmed.ncbi.nlm.nih.gov/29291729 29291729]; doi: [https://dx.doi.org/10.1186/s12870-017-1213-1 10.1186/s12870-017-1213-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29291729 20]. | #Behr M, <i>et al.</i> (2018) "Insights into the molecular regulation of monolignol-derived product biosynthesis in the growing hemp hypocotyl." <i>BMC Plant Biol</i> <b>18</b>(1):1; PMID: [https://pubmed.ncbi.nlm.nih.gov/29291729 29291729]; doi: [https://dx.doi.org/10.1186/s12870-017-1213-1 10.1186/s12870-017-1213-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29291729 20]. | ||
+ | #Bruschi M, <i>et al.</i> (2018) "Proteome of Bovine Mitochondria and Rod Outer Segment Disks: Commonalities and Differences." <i>J Proteome Res</i> <b>17</b>(2):918–925; PMID: [https://pubmed.ncbi.nlm.nih.gov/29299929 29299929]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00741 10.1021/acs.jproteome.7b00741]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29299929 9]. | ||
#Ritz D, <i>et al.</i> (2018) "Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition." <i>Proteomics</i> <b>18</b>(12):e1700246; PMID: [https://pubmed.ncbi.nlm.nih.gov/29314611 29314611]; doi: [https://dx.doi.org/10.1002/pmic.201700246 10.1002/pmic.201700246]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29314611 27]. | #Ritz D, <i>et al.</i> (2018) "Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition." <i>Proteomics</i> <b>18</b>(12):e1700246; PMID: [https://pubmed.ncbi.nlm.nih.gov/29314611 29314611]; doi: [https://dx.doi.org/10.1002/pmic.201700246 10.1002/pmic.201700246]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29314611 27]. | ||
#Kooijman S, <i>et al.</i> (2018) "Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness." <i>J Proteomics</i> <b>175</b>:144–155; PMID: [https://pubmed.ncbi.nlm.nih.gov/29317357 29317357]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.12.021 10.1016/j.jprot.2017.12.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29317357 55]. | #Kooijman S, <i>et al.</i> (2018) "Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness." <i>J Proteomics</i> <b>175</b>:144–155; PMID: [https://pubmed.ncbi.nlm.nih.gov/29317357 29317357]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.12.021 10.1016/j.jprot.2017.12.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29317357 55]. | ||
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#Wang H, <i>et al.</i> (2021) "An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism." <i>Mol Cell Proteomics</i> <b>20</b>:100141; PMID: [https://pubmed.ncbi.nlm.nih.gov/34478876 34478876]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100141 10.1016/j.mcpro.2021.100141]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34478876 6]. | #Wang H, <i>et al.</i> (2021) "An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism." <i>Mol Cell Proteomics</i> <b>20</b>:100141; PMID: [https://pubmed.ncbi.nlm.nih.gov/34478876 34478876]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100141 10.1016/j.mcpro.2021.100141]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34478876 6]. | ||
#Frankovsky J, <i>et al.</i> (2021) "The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids." <i>J Biol Chem</i> <b>297</b>(4):101155; PMID: [https://pubmed.ncbi.nlm.nih.gov/34480900 34480900]; doi: [https://dx.doi.org/10.1016/j.jbc.2021.101155 10.1016/j.jbc.2021.101155]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34480900 36]. | #Frankovsky J, <i>et al.</i> (2021) "The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids." <i>J Biol Chem</i> <b>297</b>(4):101155; PMID: [https://pubmed.ncbi.nlm.nih.gov/34480900 34480900]; doi: [https://dx.doi.org/10.1016/j.jbc.2021.101155 10.1016/j.jbc.2021.101155]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34480900 36]. | ||
+ | #Goodyear MC, <i>et al.</i> (2021) "Label-free quantitative proteomics identifies unique proteomes of clinical isolates of the Liverpool Epidemic Strain of Pseudomonas aeruginosa and laboratory strain PAO1." <i>Proteomics Clin Appl</i> <b>15</b>(6):e2100062; PMID: [https://pubmed.ncbi.nlm.nih.gov/34510773 34510773]; doi: [https://dx.doi.org/10.1002/prca.202100062 10.1002/prca.202100062]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34510773 12]. | ||
#Mukherjee S, <i>et al.</i> (2021) "Citrullination of Amyloid-β Peptides in Alzheimer's Disease." <i>ACS Chem Neurosci</i> <b>12</b>(19):3719–3732; PMID: [https://pubmed.ncbi.nlm.nih.gov/34519476 34519476]; doi: [https://dx.doi.org/10.1021/acschemneuro.1c00474 10.1021/acschemneuro.1c00474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34519476 10]. | #Mukherjee S, <i>et al.</i> (2021) "Citrullination of Amyloid-β Peptides in Alzheimer's Disease." <i>ACS Chem Neurosci</i> <b>12</b>(19):3719–3732; PMID: [https://pubmed.ncbi.nlm.nih.gov/34519476 34519476]; doi: [https://dx.doi.org/10.1021/acschemneuro.1c00474 10.1021/acschemneuro.1c00474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34519476 10]. | ||
#Zhang X, <i>et al.</i> (2021) "The Insufficient Activation of RIG-I-Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells." <i>Mol Cell Proteomics</i> <b>20</b>:100147; PMID: [https://pubmed.ncbi.nlm.nih.gov/34530158 34530158]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100147 10.1016/j.mcpro.2021.100147]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34530158 4]. | #Zhang X, <i>et al.</i> (2021) "The Insufficient Activation of RIG-I-Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells." <i>Mol Cell Proteomics</i> <b>20</b>:100147; PMID: [https://pubmed.ncbi.nlm.nih.gov/34530158 34530158]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100147 10.1016/j.mcpro.2021.100147]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34530158 4]. | ||
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#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]. | ||
#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]. | ||
#Yin H, <i>et al.</i> (2022) "A20 and ABIN-1 cooperate in balancing CBM complex-triggered NF-κB signaling in activated T cells." <i>Cell Mol Life Sci</i> <b>79</b>(2):112; PMID: [https://pubmed.ncbi.nlm.nih.gov/35099607 35099607]; doi: [https://dx.doi.org/10.1007/s00018-022-04154-z 10.1007/s00018-022-04154-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35099607 9]. | #Yin H, <i>et al.</i> (2022) "A20 and ABIN-1 cooperate in balancing CBM complex-triggered NF-κB signaling in activated T cells." <i>Cell Mol Life Sci</i> <b>79</b>(2):112; PMID: [https://pubmed.ncbi.nlm.nih.gov/35099607 35099607]; doi: [https://dx.doi.org/10.1007/s00018-022-04154-z 10.1007/s00018-022-04154-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35099607 9]. | ||
+ | #Dekker PM, <i>et al.</i> (2022) "Exploring Human Milk Dynamics: Interindividual Variation in Milk Proteome, Peptidome, and Metabolome." <i>J Proteome Res</i> <b>21</b>(4):1002–1016; PMID: [https://pubmed.ncbi.nlm.nih.gov/35104145 35104145]; doi: [https://dx.doi.org/10.1021/acs.jproteome.1c00879 10.1021/acs.jproteome.1c00879]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35104145 30]. | ||
#Krishnan RK, <i>et al.</i> (2021) "Revisiting the Role of <i>ß</i>-Tubulin in <i>Drosophila</i> Development: <i>β-tubulin60D</i> is not an Essential Gene, and its Novel <i>Pin</i> <sup><i>1</i></sup> Allele has a Tissue-Specific Dominant-Negative Impact." <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [https://pubmed.ncbi.nlm.nih.gov/35111755 35111755]; doi: [https://dx.doi.org/10.3389/fcell.2021.787976 10.3389/fcell.2021.787976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35111755 6]. | #Krishnan RK, <i>et al.</i> (2021) "Revisiting the Role of <i>ß</i>-Tubulin in <i>Drosophila</i> Development: <i>β-tubulin60D</i> is not an Essential Gene, and its Novel <i>Pin</i> <sup><i>1</i></sup> Allele has a Tissue-Specific Dominant-Negative Impact." <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [https://pubmed.ncbi.nlm.nih.gov/35111755 35111755]; doi: [https://dx.doi.org/10.3389/fcell.2021.787976 10.3389/fcell.2021.787976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35111755 6]. | ||
#Correll VL, <i>et al.</i> (2022) "Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis." <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [https://pubmed.ncbi.nlm.nih.gov/35119778 35119778]; doi: [https://dx.doi.org/10.1002/jev2.12184 10.1002/jev2.12184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35119778 9]. | #Correll VL, <i>et al.</i> (2022) "Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis." <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [https://pubmed.ncbi.nlm.nih.gov/35119778 35119778]; doi: [https://dx.doi.org/10.1002/jev2.12184 10.1002/jev2.12184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35119778 9]. | ||
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#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]. | ||
#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 | + | #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 | + | #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]. |
+ | #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]. |
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 May 15, 2022.