Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Abstract

Summary The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell-type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive and robust targeted mass spectrometric method selected reaction monitoring, SRM. This human SRMAtlas provides definitive coordinates that conclusively identify the respective peptide in biological samples. We report data on 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations and post-translational modifications. The data is freely accessible as a resource at www.srmatlas.org, and we demonstrate its utility by examining the network response to inhibition of cholesterol synthesis in liver cells and to docetaxel in prostate cancer lines.

Composition and Regulation of the Cellular Repertoire of SCF Ubiquitin Ligases

“…At least two (and in most cases three) unique tryptic peptides per protein were selected and synthesized as isotopically heavy ( 13 C 6 15 N 2 -lysine and 13 C 6 15 N 4 -arginine) standards (Table S1A). Peptides that have been observed in-house were given top priority in peptide selection, but for those that have not been observed, we used SRMAtlas (Kusebauch et al, 2016). Unpurified peptides were pooled together in a 50 pmol/peptide/µl stock.…”

The PeptideAtlas of the Domestic Laying Hen

“…59–65 One major limitation of the model is the lack of commercially available chicken specific reagents for IHC and Western Blot analysis; the use of cross-reactive human antibodies has yielded inconsistent results, especially in the case of CA125, the primary prognostic marker for human OVC. 66–68 The PeptideAtlas is a powerful resource for mining of proteotypic peptides to develop SRM-based methods 69 that can augment or replace inconsistent mRNA and IHC approaches. 70–72 Further, the current sample set is an empirical examination of the existence of many biomarkers previously unexplored by LC-MS/MS.…”

Insights into autosomal dominant polycystic kidney disease by quantitative mass spectrometry-based proteomics

“…Up to now, the knowledge of the proteotyptic peptides of potential biomarker candidate proteins to be used in targeted MS analyses has been limited, making the development of targeted proteomic assays time-and labor-intensive. Two recent impressive large-scale studies have defined protein-specific peptides for the entire human proteome to be used in targeted MS approaches (Kusebauch et al 2016;Matsumoto et al 2016). With these resources available, the development of targeted MS assays should be less time-consuming boosting their implementation in basic and translational research and in clinical diagnostics.…”