Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times.

ABSTRACT: In typical shotgun experiments, the mass spectrometer records the masses of a large set of ionized analytes but fragments only a fraction of them. In the subsequent analyses, normally only the fragmented ions are used to compile a set of peptide identifications, while the unfragmented ones are disregarded. In this work, we show how the unfragmented ions, here denoted MS1-features, can be used to increase the confidence of the proteins identified in shotgun experiments. Specifically, we propose the usage of in silico mass tags, where the observed MS1-features are matched against de novo predicted masses and retention times for all peptides derived from a sequence database. We present a statistical model to assign protein-level probabilities based on the MS1-features and combine this data wi

SUBMITTER: Moruz L 

PROVIDER: S-EPMC3860378 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature