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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 Jan | + | 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 9, 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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#Lignitto L, <i>et al.</i> (2019) "Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1." <i>Cell</i> <b>178</b>(2):316–329.e18; PMID: [https://pubmed.ncbi.nlm.nih.gov/31257023 31257023]; doi: [https://dx.doi.org/10.1016/j.cell.2019.06.003 10.1016/j.cell.2019.06.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31257023 1]. | #Lignitto L, <i>et al.</i> (2019) "Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1." <i>Cell</i> <b>178</b>(2):316–329.e18; PMID: [https://pubmed.ncbi.nlm.nih.gov/31257023 31257023]; doi: [https://dx.doi.org/10.1016/j.cell.2019.06.003 10.1016/j.cell.2019.06.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31257023 1]. | ||
#Holthenrich A, <i>et al.</i> (2019) "Proximity proteomics of endothelial Weibel-Palade bodies identifies novel regulator of von Willebrand factor secretion." <i>Blood</i> <b>134</b>(12):979–982; PMID: [https://pubmed.ncbi.nlm.nih.gov/31262780 31262780]; doi: [https://dx.doi.org/10.1182/blood.2019000786 10.1182/blood.2019000786]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31262780 12]. | #Holthenrich A, <i>et al.</i> (2019) "Proximity proteomics of endothelial Weibel-Palade bodies identifies novel regulator of von Willebrand factor secretion." <i>Blood</i> <b>134</b>(12):979–982; PMID: [https://pubmed.ncbi.nlm.nih.gov/31262780 31262780]; doi: [https://dx.doi.org/10.1182/blood.2019000786 10.1182/blood.2019000786]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31262780 12]. | ||
+ | #Abdelhamed S, <i>et al.</i> (2019) "Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche." <i>EMBO Rep</i> <b>20</b>(7):e47546; PMID: [https://pubmed.ncbi.nlm.nih.gov/31267709 31267709]; doi: [https://dx.doi.org/10.15252/embr.201847546 10.15252/embr.201847546]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31267709 26]. | ||
#Pierre N, <i>et al.</i> (2020) "Proteomics Highlights Common and Distinct Pathophysiological Processes Associated with Ileal and Colonic Ulcers in Crohn's Disease." <i>J Crohns Colitis</i> <b>14</b>(2):205–215; PMID: [https://pubmed.ncbi.nlm.nih.gov/31282946 31282946]; doi: [https://dx.doi.org/10.1093/ecco-jcc/jjz130 10.1093/ecco-jcc/jjz130]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31282946 96]. | #Pierre N, <i>et al.</i> (2020) "Proteomics Highlights Common and Distinct Pathophysiological Processes Associated with Ileal and Colonic Ulcers in Crohn's Disease." <i>J Crohns Colitis</i> <b>14</b>(2):205–215; PMID: [https://pubmed.ncbi.nlm.nih.gov/31282946 31282946]; doi: [https://dx.doi.org/10.1093/ecco-jcc/jjz130 10.1093/ecco-jcc/jjz130]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31282946 96]. | ||
#Narayan R, <i>et al.</i> (2019) "Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin." <i>PLoS One</i> <b>14</b>(7):e0219547; PMID: [https://pubmed.ncbi.nlm.nih.gov/31291378 31291378]; doi: [https://dx.doi.org/10.1371/journal.pone.0219547 10.1371/journal.pone.0219547]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31291378 86]. | #Narayan R, <i>et al.</i> (2019) "Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin." <i>PLoS One</i> <b>14</b>(7):e0219547; PMID: [https://pubmed.ncbi.nlm.nih.gov/31291378 31291378]; doi: [https://dx.doi.org/10.1371/journal.pone.0219547 10.1371/journal.pone.0219547]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31291378 86]. | ||
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#Hu Z, <i>et al.</i> (2021) "UFBP1, a key component in ufmylation, enhances drug sensitivity by promoting proteasomal degradation of oxidative stress-response transcription factor Nrf2." <i>Oncogene</i> <b>40</b>(3):647–662; PMID: [https://pubmed.ncbi.nlm.nih.gov/33219317 33219317]; doi: [https://dx.doi.org/10.1038/s41388-020-01551-1 10.1038/s41388-020-01551-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33219317 3]. | #Hu Z, <i>et al.</i> (2021) "UFBP1, a key component in ufmylation, enhances drug sensitivity by promoting proteasomal degradation of oxidative stress-response transcription factor Nrf2." <i>Oncogene</i> <b>40</b>(3):647–662; PMID: [https://pubmed.ncbi.nlm.nih.gov/33219317 33219317]; doi: [https://dx.doi.org/10.1038/s41388-020-01551-1 10.1038/s41388-020-01551-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33219317 3]. | ||
#Zaro BW, <i>et al.</i> (2020) "Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/33236985 33236985]; doi: [https://dx.doi.org/10.7554/eLife.62210 10.7554/eLife.62210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33236985 64]. | #Zaro BW, <i>et al.</i> (2020) "Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/33236985 33236985]; doi: [https://dx.doi.org/10.7554/eLife.62210 10.7554/eLife.62210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33236985 64]. | ||
+ | #Hermand P, <i>et al.</i> (2020) "The proteome of neutrophils in sickle cell disease reveals an unexpected activation of interferon alpha signaling pathway." <i>Haematologica</i> <b>105</b>(12):2851–2854; PMID: [https://pubmed.ncbi.nlm.nih.gov/33256386 33256386]; doi: [https://dx.doi.org/10.3324/haematol.2019.238295 10.3324/haematol.2019.238295]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33256386 8]. | ||
#Ouni E, <i>et al.</i> (2020) "Divide-and-Conquer Matrisome Protein (DC-MaP) Strategy: An MS-Friendly Approach to Proteomic Matrisome Characterization." <i>Int J Mol Sci</i> <b>21</b>(23):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33266304 33266304]; doi: [https://dx.doi.org/10.3390/ijms21239141 10.3390/ijms21239141]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33266304 90]. | #Ouni E, <i>et al.</i> (2020) "Divide-and-Conquer Matrisome Protein (DC-MaP) Strategy: An MS-Friendly Approach to Proteomic Matrisome Characterization." <i>Int J Mol Sci</i> <b>21</b>(23):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33266304 33266304]; doi: [https://dx.doi.org/10.3390/ijms21239141 10.3390/ijms21239141]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33266304 90]. | ||
#Braun F, <i>et al.</i> (2020) "The proteomic landscape of small urinary extracellular vesicles during kidney transplantation." <i>J Extracell Vesicles</i> <b>10</b>(1):e12026; PMID: [https://pubmed.ncbi.nlm.nih.gov/33304478 33304478]; doi: [https://dx.doi.org/10.1002/jev2.12026 10.1002/jev2.12026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33304478 89]. | #Braun F, <i>et al.</i> (2020) "The proteomic landscape of small urinary extracellular vesicles during kidney transplantation." <i>J Extracell Vesicles</i> <b>10</b>(1):e12026; PMID: [https://pubmed.ncbi.nlm.nih.gov/33304478 33304478]; doi: [https://dx.doi.org/10.1002/jev2.12026 10.1002/jev2.12026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33304478 89]. | ||
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#Bala K, <i>et al.</i> (2021) "Identification of differentially expressed proteins between fused and open sutures in sagittal nonsyndromic craniosynostosis during suture development by quantitative proteomic analysis." <i>Proteomics Clin Appl</i> <b>15</b>(2-3):e2000031; PMID: [https://pubmed.ncbi.nlm.nih.gov/33580899 33580899]; doi: [https://dx.doi.org/10.1002/prca.202000031 10.1002/prca.202000031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33580899 3]. | #Bala K, <i>et al.</i> (2021) "Identification of differentially expressed proteins between fused and open sutures in sagittal nonsyndromic craniosynostosis during suture development by quantitative proteomic analysis." <i>Proteomics Clin Appl</i> <b>15</b>(2-3):e2000031; PMID: [https://pubmed.ncbi.nlm.nih.gov/33580899 33580899]; doi: [https://dx.doi.org/10.1002/prca.202000031 10.1002/prca.202000031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33580899 3]. | ||
#Silbern I, <i>et al.</i> (2021) "Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling." <i>Mol Cell Proteomics</i> <b>20</b>:100061; PMID: [https://pubmed.ncbi.nlm.nih.gov/33582301 33582301]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100061 10.1016/j.mcpro.2021.100061]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33582301 180]. | #Silbern I, <i>et al.</i> (2021) "Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling." <i>Mol Cell Proteomics</i> <b>20</b>:100061; PMID: [https://pubmed.ncbi.nlm.nih.gov/33582301 33582301]; doi: [https://dx.doi.org/10.1016/j.mcpro.2021.100061 10.1016/j.mcpro.2021.100061]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33582301 180]. | ||
+ | #Forlani G, <i>et al.</i> (2021) "CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens." <i>Mol Cell Proteomics</i> <b>20</b>:100032; PMID: [https://pubmed.ncbi.nlm.nih.gov/33592498 33592498]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002201 10.1074/mcp.RA120.002201]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33592498 133]. | ||
#Dudek M, <i>et al.</i> (2021) "Circadian time series proteomics reveals daily dynamics in cartilage physiology." <i>Osteoarthritis Cartilage</i> <b>29</b>(5):739–749; PMID: [https://pubmed.ncbi.nlm.nih.gov/33610821 33610821]; doi: [https://dx.doi.org/10.1016/j.joca.2021.02.008 10.1016/j.joca.2021.02.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33610821 72]. | #Dudek M, <i>et al.</i> (2021) "Circadian time series proteomics reveals daily dynamics in cartilage physiology." <i>Osteoarthritis Cartilage</i> <b>29</b>(5):739–749; PMID: [https://pubmed.ncbi.nlm.nih.gov/33610821 33610821]; doi: [https://dx.doi.org/10.1016/j.joca.2021.02.008 10.1016/j.joca.2021.02.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33610821 72]. | ||
#Pietrowska M, <i>et al.</i> (2021) "Proteomic profile of melanoma cell-derived small extracellular vesicles in patients' plasma: a potential correlate of melanoma progression." <i>J Extracell Vesicles</i> <b>10</b>(4):e12063; PMID: [https://pubmed.ncbi.nlm.nih.gov/33613873 33613873]; doi: [https://dx.doi.org/10.1002/jev2.12063 10.1002/jev2.12063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33613873 30]. | #Pietrowska M, <i>et al.</i> (2021) "Proteomic profile of melanoma cell-derived small extracellular vesicles in patients' plasma: a potential correlate of melanoma progression." <i>J Extracell Vesicles</i> <b>10</b>(4):e12063; PMID: [https://pubmed.ncbi.nlm.nih.gov/33613873 33613873]; doi: [https://dx.doi.org/10.1002/jev2.12063 10.1002/jev2.12063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33613873 30]. |
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 papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
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 9, 2022.