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The Forgotten Fragments

19 October 2011  •  Author(s): Ross Chawner and Claire E. Eyers, Michael Barber Centre for Mass Spectrometry, University of Manchester

Identification of protein biomarkers and the evaluation of changes in protein expression following drug treatment rely on both the generation of peptides from cellular proteins, and the acquisition and interpretation of spectra generated by tandem mass spectrometry (MS/MS). Acquisition of MS/MS spectra in a datadependent manner means that a significant number of the protein fragments (peptides) generated are never actually subjected to MS/MS1. Moreover, only a small proportion of acquired MS/MS spectra are ever interpreted, despite the large number of tools for the automated analysis of such data. Furthermore, many fragment ions are simply ignored during data analysis, in large part because automated search engines do not ‘look’ for all potential fragmentation products, and also because we simply still do not sufficiently understand the mechanisms of gas-phase peptide fragmentation to fully interpret the spectra (most likely a combination of the two). The end result is that even though proteome coverage is increasing in large-scale analyses, we are still a long way from the ideal of ‘complete’ proteome analysis.

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