A Human Proteome Detection and Quantitation Project

N Leigh Anderson,Norman G Anderson,Terry W Pearson,Christoph H Borchers,Amanda G Paulovich,Scott D Patterson,Michael Gillette,Ruedi Aebersold,Steven A Carr

doi:10.1074/mcp.r800015-mcp200

Abstract

The lack of sensitive, specific, multiplexable assays for most human proteins is the major technical barrier impeding development of candidate biomarkers into clinically useful tests. Recent progress in mass spectrometry-based assays for proteotypic peptides, particularly those with specific affinity peptide enrichment, offers a systematic and economical path to comprehensive quantitative coverage of the human proteome. A complete suite of assays, e.g. two peptides from the protein product of each of the approximately 20,500 human genes (here termed the human Proteome Detection and Quantitation project), would enable rapid and systematic verification of candidate biomarkers and lay a quantitative foundation for subsequent efforts to define the larger universe of splice variants, post-translational modifications, protein-protein interactions, and tissue localization.

Highlights

The lack of sensitive, specific, multiplexable assays for most human proteins is the major technical barrier impeding development of candidate biomarkers into clinically useful tests
Major challenges in defining a comprehensive Human Proteome Project are 1) the potentially very large number of proteins with modified forms; 2) the diversity of technology platforms involved in their study; 3) the variety of overlapping biological “units” into which the proteome might be divided for organized conquest; and 4) sensitivity limitations in detecting proteins present in trace amounts
We propose a near-term tactical approach, called the human Proteome Detection and Quantitation1 project that will enable measurement of the human proteome in a way that would yield immediately useful results while the strategy for a comprehensive Human Proteome Project is worked out

Summary

Introduction

The lack of sensitive, specific, multiplexable assays for most human proteins is the major technical barrier impeding development of candidate biomarkers into clinically useful tests. The goal of the hPDQ is to enable individual biological researchers to measure defined collections of human proteins in biological samples with 1 ng/ml sensitivity and absolute specificity, at throughput and cost levels that permit the study of meaningfully large biological populations (ϳ500 –5,000 samples).

Results

Conclusion