Journal
GENOMICS PROTEOMICS & BIOINFORMATICS
Volume 13, Issue 1, Pages 25-35Publisher
ELSEVIER
DOI: 10.1016/j.gpb.2014.11.002
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Funding
- NCRR NIH HHS [1S10RR026707-01, S10 RR026707, UL1 RR024139] Funding Source: Medline
- NIA NIH HHS [P50 AG047270] Funding Source: Medline
- NIDA NIH HHS [P30 DA018343, P30DA018343] Funding Source: Medline
- NIDDK NIH HHS [K01 DK089006] Funding Source: Medline
- NIH HHS [S10 OD018034, 1S10OD018034-01] Funding Source: Medline
- PHS HHS [NIDDK-K01DK089006] Funding Source: Medline
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We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
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