YPED: an Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

Overview

Journal Genomics Proteomics Bioinformatics

Specialty Biology

Date 2015 Feb 26

PMID 25712262

Citations 9

Authors

Christopher M Colangelo

Mark Shifman

Kei-Hoi Cheung

Kathryn L Stone

Nicholas J Carriero

Erol E Gulcicek

TuKiet T Lam

Terence Wu

Robert D Bjornson

Can Bruce

Angus C Nairn

Jesse Rinehart

Perry L Miller

Kenneth R Williams

Affiliations

Soon will be listed here.

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.

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