Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis.

ABSTRACT: The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investi

SUBMITTER: Leon IR 

PROVIDER: S-EPMC3790306 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature