Effects of modified digestion schemes on the identification of proteins from complex mixtures.

Journal of Proteome Research
Aaron A Klammer, Michael J MacCoss

Abstract

In shotgun proteomics, a complex protein mixture is digested to peptides, separated, and identified by microcapillary liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this technology, complete protein digestion is often assumed. We show that, to the contrary, modifications to a standard digestion protocol demonstrate large, reproducible improvements in protein identification, a result consistent with digestion being a limiting factor in the efficiency of protein identification.

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