A HUPO Test Sample Study Reveals Common Problems in Mass Spectrometry-based Proteomics

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2009 May 19

PMID 19448641

Citations 132

Authors

Alexander W Bell

Eric W Deutsch

Catherine E Au

Robert E Kearney

Ron Beavis

Salvatore Sechi

Tommy Nilsson

John J M Bergeron

Affiliations

Soon will be listed here.

Abstract

We performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics.

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