A test for mass spectrometer fragmentation

Proteins and their building blocks, peptides, form the machinery of cellular physiology, regulating and executing virtually all processes of life. Proteomics relies on mass spectrometer devices for identifying and quantifying peptides.

IMSB researchers have developed a mathematical toolset to benchmark the precision and reproducibility of the peptide fragmentation processes happening in a mass spectrometer (Toprak, U. H. et al. (2014) Molecular & cellular proteomics: MCP 13,Proteomics mcp.O113.036475). This method was applied to compare different mass spectrometers of different generations and product families. The results confirm the expected superiority of the latest generation mass spectrometers and methodologies, notably the targeted extraction of SWATH-MS datasets previously introduced by the Aebersold lab (Gillet, L. C. et al. (2012) Molecular & cellular proteomics: MCP 11, O111 016717). The code used for obtaining the results presented in this study have been made available to the community as an open-source python script toolset.

This paper may be quoted if you need a reference for:

• The importance of good spectral similarity measures in targeted proteomics (SRM or SWATH)

• The intrinsic reproducibility of the peptide fragmentation within a given instrument (Orbi-Elite being the best)

• The assessment of assay portability from one instrument to another (5600-Shotgun to 5600-SWATH being the best)

• The use of naked peptide assays to mine for modified peptides in targeted proteomics (shown in for phospho-peptides in the study)
  

Reference: Toprak UH, Gillet LC, Maiolica A, Navarro P, Leitner A, Aebersold R. Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics. Mol Cell Proteomics. 2014 Mar 12