PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

Abstract

A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the system being studied. For proteomics to be a key part of such studies, it must deliver accurate quantification of all the components in the system for each tested perturbation without any gaps in the data. This will require a new approach to proteomics that is based on emerging targeted quantitative mass spectrometry techniques. The PeptideAtlas Project comprises a growing, publicly accessible database of peptides identified in many tandem mass spectrometry proteomics studies and software tools that allow the building of PeptideAtlas, as well as its use by the research community. Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.

Figure 1

An overview of the build process of PeptideAtlas. Shotgun tandem mass spectrometry (MS/MS) experimental data are contributed by the community to the PeptideAtlas raw data repository, which is linked to other repositories by the ProteomExchange consortium. The raw data are processed through an evolving but consistent analysis and validation pipeline (Trans Proteomic Pipeline (TPP)) and loaded into the PeptideAtlas database, and made available to the community. Tranche, Global Proteome Machine Database (GPMDB), National Institute of Standards and Technology (NIST) and Protein Identifications Database (PRIDE) are currently the main participants in the ProteomExchange consortium.

Figure 2

An overview of the features provided by PeptideAtlas that allow targeted proteomics workflows. PeptideAtlas and its specialized builds, Unipep (containing N-glycosylation sites) and PhosphoPep (containing phosphorylation sites), allow the community to: select proteotypic peptides for targeting; select SRM transitions for targeting; annotate and view annotations for these peptides and transitions; visualize peptides and proteins with Cytoscape; interface with Targeted Identification for Quantitative Analysis by MRM (TIQAM) for experimental design; obtain approximate protein abundances for spiking in synthetic peptides; obtain spectrum libraries for search and verification; and download PeptideAtlas builds for new projects. MRM, multiple reaction monitoring; SRM, selected reaction monitoring.

Eric W. Deutsch

Henry Lam

Ruedi Aebersold