Integrating shotgun proteomics and mRNA expression data to improve protein identification.

ABSTRACT:

Motivation

Tandem mass spectrometry (MS/MS) offers fast and reliable characterization of complex protein mixtures, but suffers from low sensitivity in protein identification. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration.

Results

We develop a Bayesian score that estimates the posterior probability of a protein's presence in the sample given its identification in an MS/MS experiment and its mRNA concentration measured under similar experimental conditions. Our method, MSpresso, substantially increases the number of proteins identified in an MS/MS experiment at the sa

SUBMITTER: Ramakrishnan SR 

PROVIDER: S-EPMC2682515 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature