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Genomics Proteomics Bioinformatics. 2015 Feb;13(1):25-35. doi: 10.1016/j.gpb.2014.11.002. Epub 2015 Feb 21.

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

Author information

1
W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA. Electronic address: christopher.colangelo@yale.edu.
2
Yale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT 06510, USA.
3
Yale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Emergency Medicine, School of Medicine, Yale University, New Haven, CT 06510, USA; VA Connecticut Healthcare System, West Haven, CT 06516, USA.
4
W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
5
W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale Center for Genome Analysis, West Campus, Yale University, Orange, CT 06477, USA.
6
W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; Yale West Campus Analytical Core, West Campus, Yale University, West Haven, CT 06516, USA.
7
W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; Yale Bioinformatics Resource, School of Medicine, Yale University, New Haven, CT 06510, USA.
8
Department of Psychiatry, School of Medicine, Yale University, New Haven, CT 06510, USA.
9
Department of Cellular & Molecular Physiology, School of Medicine, Yale University, New Haven, CT 06510, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
10
Yale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT 06510, USA; VA Connecticut Healthcare System, West Haven, CT 06516, USA.

Abstract

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.

KEYWORDS:

Bioinformatics; Database; Mass spectrometry; Proteomics; Repository; Spectral library

PMID:
25712262
PMCID:
PMC4411476
DOI:
10.1016/j.gpb.2014.11.002
[Indexed for MEDLINE]
Free PMC Article
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