Protein identification as an information retrieval problem

Yiming Yang, Subramaniam Ganapathy, Abhay Harpale

Abstract: We present the first interdisciplinary work on transforming a popular problem in proteomics, i.e. protein identification from tandem mass spectra, to an Information Retrieval (IR) problem. We present an empirical comparison of popular IR approaches, such as those available from Indri and Lemur toolkits on benchmark datasets, to representative popular baselines in the proteomics literature. Our experiments demonstrate statistically significant evidence that popular IR approaches outperform representative baseline approaches in proteomics.