GPMDB Data Sources

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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 5, 2022.
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) &quot;Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.&quot; <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049&ndash;54; PMID: [ 12177431]; doi: [ 10.1073/pnas.172170199]; GPMDB: [ 498].
#Lipton MS, <i>et al.</i> (2002) &quot;Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.&quot; <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049&ndash;54; PMID: [ 12177431]; doi: [ 10.1073/pnas.172170199]; GPMDB: [ 498].
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#Kelley RC, <i>et al.</i> (2018) &quot;Advanced aging causes diaphragm functional abnormalities, global proteome remodeling, and loss of mitochondrial cysteine redox flexibility in mice.&quot; <i>Exp Gerontol</i> <b>103</b>:69&ndash;79; PMID: [ 29289553]; doi: [ 10.1016/j.exger.2017.12.017]; GPMDB: [ 24].
#Kelley RC, <i>et al.</i> (2018) &quot;Advanced aging causes diaphragm functional abnormalities, global proteome remodeling, and loss of mitochondrial cysteine redox flexibility in mice.&quot; <i>Exp Gerontol</i> <b>103</b>:69&ndash;79; PMID: [ 29289553]; doi: [ 10.1016/j.exger.2017.12.017]; GPMDB: [ 24].
#Behr M, <i>et al.</i> (2018) &quot;Insights into the molecular regulation of monolignol-derived product biosynthesis in the growing hemp hypocotyl.&quot; <i>BMC Plant Biol</i> <b>18</b>(1):1; PMID: [ 29291729]; doi: [ 10.1186/s12870-017-1213-1]; GPMDB: [ 20].
#Behr M, <i>et al.</i> (2018) &quot;Insights into the molecular regulation of monolignol-derived product biosynthesis in the growing hemp hypocotyl.&quot; <i>BMC Plant Biol</i> <b>18</b>(1):1; PMID: [ 29291729]; doi: [ 10.1186/s12870-017-1213-1]; GPMDB: [ 20].
#Bruschi M, <i>et al.</i> (2018) &quot;Proteome of Bovine Mitochondria and Rod Outer Segment Disks: Commonalities and Differences.&quot; <i>J Proteome Res</i> <b>17</b>(2):918&ndash;925; PMID: [ 29299929]; doi: [ 10.1021/acs.jproteome.7b00741]; GPMDB: [ 9].
#Ritz D, <i>et al.</i> (2018) &quot;Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition.&quot; <i>Proteomics</i> <b>18</b>(12):e1700246; PMID: [ 29314611]; doi: [ 10.1002/pmic.201700246]; GPMDB: [ 27].
#Ritz D, <i>et al.</i> (2018) &quot;Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition.&quot; <i>Proteomics</i> <b>18</b>(12):e1700246; PMID: [ 29314611]; doi: [ 10.1002/pmic.201700246]; GPMDB: [ 27].
#Kooijman S, <i>et al.</i> (2018) &quot;Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness.&quot; <i>J Proteomics</i> <b>175</b>:144&ndash;155; PMID: [ 29317357]; doi: [ 10.1016/j.jprot.2017.12.021]; GPMDB: [ 55].
#Kooijman S, <i>et al.</i> (2018) &quot;Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness.&quot; <i>J Proteomics</i> <b>175</b>:144&ndash;155; PMID: [ 29317357]; doi: [ 10.1016/j.jprot.2017.12.021]; GPMDB: [ 55].
Line 2,493: Line 2,494:
#Wang H, <i>et al.</i> (2021) &quot;An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism.&quot; <i>Mol Cell Proteomics</i> <b>20</b>:100141; PMID: [ 34478876]; doi: [ 10.1016/j.mcpro.2021.100141]; GPMDB: [ 6].
#Wang H, <i>et al.</i> (2021) &quot;An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism.&quot; <i>Mol Cell Proteomics</i> <b>20</b>:100141; PMID: [ 34478876]; doi: [ 10.1016/j.mcpro.2021.100141]; GPMDB: [ 6].
#Frankovsky J, <i>et al.</i> (2021) &quot;The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids.&quot; <i>J Biol Chem</i> <b>297</b>(4):101155; PMID: [ 34480900]; doi: [ 10.1016/j.jbc.2021.101155]; GPMDB: [ 36].
#Frankovsky J, <i>et al.</i> (2021) &quot;The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids.&quot; <i>J Biol Chem</i> <b>297</b>(4):101155; PMID: [ 34480900]; doi: [ 10.1016/j.jbc.2021.101155]; GPMDB: [ 36].
#Goodyear MC, <i>et al.</i> (2021) &quot;Label-free quantitative proteomics identifies unique proteomes of clinical isolates of the Liverpool Epidemic Strain of Pseudomonas aeruginosa and laboratory strain PAO1.&quot; <i>Proteomics Clin Appl</i> <b>15</b>(6):e2100062; PMID: [ 34510773]; doi: [ 10.1002/prca.202100062]; GPMDB: [ 12].
#Mukherjee S, <i>et al.</i> (2021) &quot;Citrullination of Amyloid-&beta; Peptides in Alzheimer&#39;s Disease.&quot; <i>ACS Chem Neurosci</i> <b>12</b>(19):3719&ndash;3732; PMID: [ 34519476]; doi: [ 10.1021/acschemneuro.1c00474]; GPMDB: [ 10].
#Mukherjee S, <i>et al.</i> (2021) &quot;Citrullination of Amyloid-&beta; Peptides in Alzheimer&#39;s Disease.&quot; <i>ACS Chem Neurosci</i> <b>12</b>(19):3719&ndash;3732; PMID: [ 34519476]; doi: [ 10.1021/acschemneuro.1c00474]; GPMDB: [ 10].
#Zhang X, <i>et al.</i> (2021) &quot;The Insufficient Activation of RIG-I-Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells.&quot; <i>Mol Cell Proteomics</i> <b>20</b>:100147; PMID: [ 34530158]; doi: [ 10.1016/j.mcpro.2021.100147]; GPMDB: [ 4].
#Zhang X, <i>et al.</i> (2021) &quot;The Insufficient Activation of RIG-I-Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells.&quot; <i>Mol Cell Proteomics</i> <b>20</b>:100147; PMID: [ 34530158]; doi: [ 10.1016/j.mcpro.2021.100147]; GPMDB: [ 4].
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#Erber L, <i>et al.</i> (2022) &quot;Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells.&quot; <i>Molecules</i> <b>27</b>(2):; PMID: [ 35056799]; doi: [ 10.3390/molecules27020484]; GPMDB: [ 24].
#Erber L, <i>et al.</i> (2022) &quot;Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells.&quot; <i>Molecules</i> <b>27</b>(2):; PMID: [ 35056799]; doi: [ 10.3390/molecules27020484]; GPMDB: [ 24].
#Ali N, <i>et al.</i> (2022) &quot;Proteomics profiling of human synovial fluid suggests increased protein interplay in early-osteoarthritis (OA) that is lost in late-stage OA.&quot; <i>Mol Cell Proteomics</i> <b></b>:100200; PMID: [ 35074580]; doi: [ 10.1016/j.mcpro.2022.100200]; GPMDB: [ 61].
#Ali N, <i>et al.</i> (2022) &quot;Proteomics profiling of human synovial fluid suggests increased protein interplay in early-osteoarthritis (OA) that is lost in late-stage OA.&quot; <i>Mol Cell Proteomics</i> <b></b>:100200; PMID: [ 35074580]; doi: [ 10.1016/j.mcpro.2022.100200]; GPMDB: [ 61].
#Garcia-Marques F, <i>et al.</i> (2022) &quot;Protein signatures to distinguish aggressive from indolent prostate cancer.&quot; <i>Prostate</i> <b>82</b>(5):605&ndash;616; PMID: [ 35098564]; doi: [ 10.1002/pros.24307]; GPMDB: [ 132].
#Yin H, <i>et al.</i> (2022) &quot;A20 and ABIN-1 cooperate in balancing CBM complex-triggered NF-&kappa;B signaling in activated T cells.&quot; <i>Cell Mol Life Sci</i> <b>79</b>(2):112; PMID: [ 35099607]; doi: [ 10.1007/s00018-022-04154-z]; GPMDB: [ 9].
#Yin H, <i>et al.</i> (2022) &quot;A20 and ABIN-1 cooperate in balancing CBM complex-triggered NF-&kappa;B signaling in activated T cells.&quot; <i>Cell Mol Life Sci</i> <b>79</b>(2):112; PMID: [ 35099607]; doi: [ 10.1007/s00018-022-04154-z]; GPMDB: [ 9].
#Dekker PM, <i>et al.</i> (2022) &quot;Exploring Human Milk Dynamics: Interindividual Variation in Milk Proteome, Peptidome, and Metabolome.&quot; <i>J Proteome Res</i> <b>21</b>(4):1002&ndash;1016; PMID: [ 35104145]; doi: [ 10.1021/acs.jproteome.1c00879]; GPMDB: [ 30].
#Krishnan RK, <i>et al.</i> (2021) &quot;Revisiting the Role of <i>&szlig;</i>-Tubulin in <i>Drosophila</i> Development: <i>&beta;-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.&quot; <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [ 35111755]; doi: [ 10.3389/fcell.2021.787976]; GPMDB: [ 6].
#Krishnan RK, <i>et al.</i> (2021) &quot;Revisiting the Role of <i>&szlig;</i>-Tubulin in <i>Drosophila</i> Development: <i>&beta;-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.&quot; <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [ 35111755]; doi: [ 10.3389/fcell.2021.787976]; GPMDB: [ 6].
#Correll VL, <i>et al.</i> (2022) &quot;Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis.&quot; <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [ 35119778]; doi: [ 10.1002/jev2.12184]; GPMDB: [ 9].
#Correll VL, <i>et al.</i> (2022) &quot;Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis.&quot; <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [ 35119778]; doi: [ 10.1002/jev2.12184]; GPMDB: [ 9].
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#McCullough EL, <i>et al.</i> (2022) &quot;The life history of <i>Drosophila</i> sperm involves molecular continuity between male and female reproductive tracts.&quot; <i>Proc Natl Acad Sci U S A</i> <b>119</b>(11):e2119899119; PMID: [ 35254899]; doi: [ 10.1073/pnas.2119899119]; GPMDB: [ 95].
#McCullough EL, <i>et al.</i> (2022) &quot;The life history of <i>Drosophila</i> sperm involves molecular continuity between male and female reproductive tracts.&quot; <i>Proc Natl Acad Sci U S A</i> <b>119</b>(11):e2119899119; PMID: [ 35254899]; doi: [ 10.1073/pnas.2119899119]; GPMDB: [ 95].
#Krumm J, <i>et al.</i> (2022) &quot;High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development.&quot; <i>Cell Rep</i> <b>38</b>(13):110604; PMID: [ 35354033]; doi: [ 10.1016/j.celrep.2022.110604]; GPMDB: [ 490].
#Krumm J, <i>et al.</i> (2022) &quot;High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development.&quot; <i>Cell Rep</i> <b>38</b>(13):110604; PMID: [ 35354033]; doi: [ 10.1016/j.celrep.2022.110604]; GPMDB: [ 490].
#Croon M, <i>et al.</i> (2022) &quot;FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction.&quot; <i>Sci Adv</i> <b>8</b>(14):eabn7105; PMID: [ 35385313]; doi: [ 10.1126/sciadv.abn7105]; GPMDB: [ 39].
#Croon M, <i>et al.</i> (2022) &quot;FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction.&quot; <i>Sci Adv</i> <b>8</b>(14):eabn7105; PMID: [ 35385313]; doi: [ 10.1126/sciadv.abn7105]; GPMDB: [ 71].
#Ubaida-Mohien C, <i>et al.</i> (2022) &quot;Unbiased proteomics, histochemistry, and mitochondrial DNA copy number reveal better mitochondrial health in muscle of high functioning octogenarians.&quot; <i>Elife</i>; PMID: [ 35404238]; doi: [ 10.7554/eLife.74335]; GPMDB: [ 65].
#Ubaida-Mohien C, <i>et al.</i> (2022) &quot;Unbiased proteomics, histochemistry, and mitochondrial DNA copy number reveal better mitochondrial health in muscle of high functioning octogenarians.&quot; <i>Elife</i>; PMID: [ 35404238]; doi: [ 10.7554/eLife.74335]; GPMDB: [ 98].
#Fernando M, <i>et al.</i> (2022) &quot;Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin.&quot; <i>Stem Cell Reports</i>; PMID: [ 35523177]; doi: [ 10.1016/j.stemcr.2022.04.003]; GPMDB: [ 117].

Latest revision as of 19:05, 15 May 2022

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.


Current Public Data Sources

The following public data repositories are checked daily for new suitable raw data for reanalysis:

  1. ProteomeXchange/PRIDE;
  2. JPOST;
  4. PeptideAtlas/PASSEL;
  5. ProteomicsDB;
  6. The Chorus Project; and
  7. iProX.

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.

Previous Data Sources

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.

Review process

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.

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 15, 2022.

  1. Lipton MS, et al. (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." Proc Natl Acad Sci U S A 99(17):11049–54; PMID: 12177431; doi: 10.1073/pnas.172170199; GPMDB: 498.
  2. Liu T, et al. (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Anal Chem 76(18):5345–53; PMID: 15362891; doi: 10.1021/ac049485q; GPMDB: 6.
  3. Sauer G, et al. (2005) "Proteome analysis of the human mitotic spindle." Mol Cell Proteomics 4(1):35–43; PMID: 15561729; doi: 10.1074/mcp.M400158-MCP200; GPMDB: 1.
  4. Klein C, et al. (2005) "The membrane proteome of Halobacterium salinarum." Proteomics 5(1):180–97; PMID: 15619294; doi: 10.1002/pmic.200400943; GPMDB: 37.
  5. Searle BC, et al. (2005) "Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm." J Proteome Res 4(2):546–54; PMID: 15822933; doi: 10.1021/pr049781j; GPMDB: 4.
  6. Elias JE, et al. (2005) "Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations." Nat Methods 2(9):667–75; PMID: 16118637; doi: 10.1038/nmeth785; GPMDB: 30.
  7. Lee YJ, et al. (2006) "Proteome analysis of human hair shaft: from protein identification to posttranslational modification." Mol Cell Proteomics 5(5):789–800; PMID: 16446289; doi: 10.1074/mcp.M500278-MCP200; GPMDB: 75.
  8. Gatlin CL, et al. (2006) "Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus." Proteomics 6(5):1530–49; PMID: 16470658; doi: 10.1002/pmic.200500253; GPMDB: 1603.
  9. Keshamouni VG, et al. (2006) "Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype." J Proteome Res 5(5):1143–54; PMID: 16674103; doi: 10.1021/pr050455t; GPMDB: 3.
  10. Bisle B, et al. (2006) "Quantitative profiling of the membrane proteome in a halophilic archaeon." Mol Cell Proteomics 5(9):1543–58; PMID: 16804162; doi: 10.1074/mcp.M600106-MCP200; GPMDB: 32.
  11. Hamacher M, et al. (2006) "HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy." Proteomics 6(18):4890–8; PMID: 16927433; doi: 10.1002/pmic.200600295; GPMDB: 296.
  12. Beausoleil SA, et al. (2006) "A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Nat Biotechnol 24(10):1285–92; PMID: 16964243; doi: 10.1038/nbt1240; GPMDB: 31.
  13. Whitehead K, et al. (2006) "An integrated systems approach for understanding cellular responses to gamma radiation." Mol Syst Biol 2:47; PMID: 16969339; doi: 10.1038/msb4100091; GPMDB: 27.
  14. Price TS, et al. (2007) "EBP, a program for protein identification using multiple tandem mass spectrometry datasets." Mol Cell Proteomics 6(3):527–36; PMID: 17164401; doi: 10.1074/mcp.T600049-MCP200; GPMDB: 314.
  15. Tanner S, et al. (2007) "Improving gene annotation using peptide mass spectrometry." Genome Res 17(2):231–9; PMID: 17189379; doi: 10.1101/gr.5646507; GPMDB: 1.
  16. Konstantinidis K, et al. (2007) "Genome-wide proteomics of Natronomonas pharaonis." J Proteome Res 6(1):185–93; PMID: 17203963; doi: 10.1021/pr060352q; GPMDB: 176.
  17. Villén J, et al. (2007) "Large-scale phosphorylation analysis of mouse liver." Proc Natl Acad Sci U S A 104(5):1488–93; PMID: 17242355; doi: 10.1073/pnas.0609836104; GPMDB: 1.
  18. Klein C, et al. (2007) "The low molecular weight proteome of Halobacterium salinarum." J Proteome Res 6(4):1510–8; PMID: 17326674; doi: 10.1021/pr060634q; GPMDB: 10.
  19. Asara JM, et al. (2007) "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry." Science 316(5822):280–5; PMID: 17431180; doi: 10.1126/science.1137614; GPMDB: 2.
  20. Lowery DM, et al. (2007) "Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate." EMBO J 26(9):2262–73; PMID: 17446864; doi: 10.1038/sj.emboj.7601683; GPMDB: 24.
  21. Brunner E, et al. (2007) "A high-quality catalog of the Drosophila melanogaster proteome." Nat Biotechnol 25(5):576–83; PMID: 17450130; doi: 10.1038/nbt1300; GPMDB: 1907.
  22. Wu L, et al. (2007) "Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling." Mol Cell Proteomics 6(8):1343–53; PMID: 17519225; doi: 10.1074/mcp.M700017-MCP200; GPMDB: 2299.
  23. Au CE, et al. (2007) "Organellar proteomics to create the cell map." Curr Opin Cell Biol 19(4):376–85; PMID: 17689063; doi: 10.1016/; GPMDB: 4090.
  24. Whiteaker JR, et al. (2007) "Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer." J Proteome Res 6(10):3962–75; PMID: 17711321; doi: 10.1021/pr070202v; GPMDB: 84.
  25. Bantscheff M, et al. (2007) "Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors." Nat Biotechnol 25(9):1035–44; PMID: 17721511; doi: 10.1038/nbt1328; GPMDB: 729.
  26. Padliya ND, et al. (2007) "Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences." Proteomics 7(21):3932–42; PMID: 17922518; doi: 10.1002/pmic.200700419; GPMDB: 1.
  27. Rikova K, et al. (2007) "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer." Cell 131(6):1190–203; PMID: 18083107; doi: 10.1016/j.cell.2007.11.025; GPMDB: 104.
  28. Ansong C, et al. (2008) "Proteomics analysis of the causative agent of typhoid fever." J Proteome Res 7(2):546–57; PMID: 18166006; doi: 10.1021/pr070434u; GPMDB: 313.
  29. Finney GL, et al. (2008) "Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data." Anal Chem 80(4):961–71; PMID: 18189369; doi: 10.1021/ac701649e; GPMDB: 12.
  30. Stevens SM Jr, et al. (2008) "Proteomic analysis of mouse brain microsomes: identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system." J Proteome Res 7(3):1046–54; PMID: 18271522; doi: 10.1021/pr7006279; GPMDB: 4.
  31. Yocum AK, et al. (2008) "Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation." Mol Cell Proteomics 7(4):750–67; PMID: 18304949; doi: 10.1074/mcp.M700399-MCP200; GPMDB: 18.
  32. Lemeer S, et al. (2008) "Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo." J Proteome Res 7(4):1555–64; PMID: 18307296; doi: 10.1021/pr700667w; GPMDB: 148.
  33. Zhai B, et al. (2008) "Phosphoproteome analysis of Drosophila melanogaster embryos." J Proteome Res 7(4):1675–82; PMID: 18327897; doi: 10.1021/pr700696a; GPMDB: 24.
  34. Denny P, et al. (2008) "The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions." J Proteome Res 7(5):1994–2006; PMID: 18361515; doi: 10.1021/pr700764j; GPMDB: 102.
  35. Simó C, et al. (2008) "Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 1. Behavior of mono- to hexapeptides." Anal Chem 80(10):3547–56; PMID: 18399644; doi: 10.1021/ac702635v; GPMDB: 19.
  36. Bachi A, et al. (2008) "Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 2. Behavior of resins containing individual amino acids." Anal Chem 80(10):3557–65; PMID: 18410134; doi: 10.1021/ac8001353; GPMDB: 2.
  37. Baerenfaller K, et al. (2008) "Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics." Science 320(5878):938–41; PMID: 18436743; doi: 10.1126/science.1157956; GPMDB: 28.
  38. Ji H, et al. (2008) "Difference gel electrophoresis analysis of Ras-transformed fibroblast cell-derived exosomes." Electrophoresis 29(12):2660–71; PMID: 18494037; doi: 10.1002/elps.200800015; GPMDB: 26.
  39. Cao Z, et al. (2008) "Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis." Mol Cell Proteomics 7(9):1651–67; PMID: 18504258; doi: 10.1074/mcp.M700155-MCP200; GPMDB: 6.
  40. Lemeer S, et al. (2008) "Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos." Mol Cell Proteomics 7(11):2176–87; PMID: 18550893; doi: 10.1074/mcp.M800081-MCP200; GPMDB: 31.
  41. Sodek KL, et al. (2008) "Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT)." Mol Biosyst 4(7):762–73; PMID: 18563251; doi: 10.1039/b717542f; GPMDB: 252.
  42. Schimmel J, et al. (2008) "The ubiquitin-proteasome system is a key component of the SUMO-2/3 cycle." Mol Cell Proteomics 7(11):2107–22; PMID: 18565875; doi: 10.1074/mcp.M800025-MCP200; GPMDB: 5.
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