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Open Access Research article

Metaprotein expression modeling for label-free quantitative proteomics

Joseph E Lucas1*, J Will Thompson1, Laura G Dubois1, Jeanette McCarthy1, Hans Tillmann2, Alexander Thompson2, Norah Shire3, Ron Hendrickson3, Francisco Dieguez3, Phyllis Goldman3, Kathleen Schwarz4, Keyur Patel2, John McHutchison2 and M Arthur Moseley1

Author Affiliations

1 Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA

2 Gasteroenterology, Duke University School of Medicine, Durham, NC, USA

3 Merck, Sharpe, and Dohme, Corp, Whitehouse Station, NJ, USA

4 Johns Hopkins Children’s Center, Baltimore, MD, USA

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BMC Bioinformatics 2012, 13:74  doi:10.1186/1471-2105-13-74

Published: 4 May 2012



Label-free quantitative proteomics holds a great deal of promise for the future study of both medicine and biology. However, the data generated is extremely intricate in its correlation structure, and its proper analysis is complex. There are issues with missing identifications. There are high levels of correlation between many, but not all, of the peptides derived from the same protein. Additionally, there may be systematic shifts in the sensitivity of the machine between experiments or even through time within the duration of a single experiment.


We describe a hierarchical model for analyzing unbiased, label-free proteomics data which utilizes the covariance of peptide expression across samples as well as MS/MS-based identifications to group peptides—a strategy we call metaprotein expression modeling. Our metaprotein model acknowledges the possibility of misidentifications, post-translational modifications and systematic differences between samples due to changes in instrument sensitivity or differences in total protein concentration. In addition, our approach allows us to validate findings from unbiased, label-free proteomics experiments with further unbiased, label-free proteomics experiments. Finally, we demonstrate the clinical/translational utility of the model for building predictors capable of differentiating biological phenotypes as well as for validating those findings in the context of three novel cohorts of patients with Hepatitis C.


Mass-spectrometry proteomics is quickly becoming a powerful tool for studying biological and translational questions. Making use of all of the information contained in a particular set of data will be critical to the success of those endeavors. Our proposed model represents an advance in the ability of statistical models of proteomic data to identify and utilize correlation between features. This allows validation of predictors without translation to targeted assays in addition to informing the choice of targets when it is appropriate to generate those assays.

Proteomics; Factor; Hepatitis; Open platform; Statistics; Statistical model; Srm; Mrm