The PeptideAtlas project

Abstract

The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. PeptideAtlas () addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.

Introns in UTRs: Why we should stop ignoring them

“…In 2004, Hillman et al [52] analyzed 1,363 human protein sequences deposited into the SwissProt database and found 107 entries (7.9% of those analyzed) that were derived from transcripts that are apparently subject to NMD. More recently an analysis of mass spectrometry data from the Global Proteome Machine [53] and PeptideAtlas [54] repositories reached the same conclusion: 3UI-containing transcripts can indeed express protein [55]. These results suggest that either the peptides detected in the above proteomics studies are the products of a single round of translation [37], or some endogenous human NMD substrates can undergo multiple rounds of translation prior to being decayed.…”

Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry

“…This software was developed from a large catalog of peptide spectra from human heart [22]. Interrogation of enormous amounts of shot-gun LC-MS/MS data in public repositories containing information on the most commonly observed peptides can assist in the determination of which peptides to use for MRM-MS analyses if annotated correctly [15,57]. Furthermore, investigations into fragment ion intensities typical in MS/MS spectra has provided useful information on potential tandem MS sequence ions.…”

Development and validation of a spectral library searching method for peptide identification from MS/MS

“…For the spectral library to be comprehensive (containing sufficient entries to cover a high proportion of the observed proteome) and accurate (containing high-quality and truly characteristic MS/MS spectra that can be confidently mapped to peptides), it is important to gather raw MS/MS spectra from a wide variety of sources, to identify them as accurately as possible, to filter out the inevitable false positives, and to process the spectra to reduce noise and other experimental artifacts. Such an endeavor is undertaken by the National Institute of Standards and Technology (NIST), in collaboration with the PeptideAtlas project of our group [24,29]. The resulting highquality spectral libraries were then used for spectral searching in this study.…”