title: YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.
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.
authors.affiliation: 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.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Colangelo
authors.affiliation: 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.
authors.forename: Mark
authors.initials: M
authors.lastname: Shifman
authors.affiliation: 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.
authors.forename: Kei-Hoi
authors.initials: KH
authors.lastname: Cheung
authors.affiliation: 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.
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Stone
authors.affiliation: 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.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Carriero
authors.affiliation: 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.
authors.forename: Erol E
authors.initials: EE
authors.lastname: Gulcicek
authors.affiliation: 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.
authors.forename: TuKiet T
authors.initials: TT
authors.lastname: Lam
authors.affiliation: 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.
authors.forename: Terence
authors.initials: T
authors.lastname: Wu
authors.affiliation: 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.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Bjornson
authors.affiliation: 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.
authors.forename: Can
authors.initials: C
authors.lastname: Bruce
authors.affiliation: Department of Psychiatry, School of Medicine, Yale University, New Haven, CT 06510, USA.
authors.forename: Angus C
authors.initials: AC
authors.lastname: Nairn
authors.affiliation: 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.
authors.forename: Jesse
authors.initials: J
authors.lastname: Rinehart
authors.affiliation: 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.
authors.forename: Perry L
authors.initials: PL
authors.lastname: Miller
authors.affiliation: 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.
authors.forename: Kenneth R
authors.initials: KR
authors.lastname: Williams
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D010446:Peptide Fragments / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010446:Peptide Fragments; D020543:Proteome
keywords: Bioinformatics; Database; Mass spectrometry; Proteomics; Repository; Spectral library