Protein identification as an information retrieval problem

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. Categories and Subject Descriptors H.4.m [Information Systems Applications]: Miscellaneous; I.5.2 General Terms Algorithms, Design, Experimentation, Performance Keywords Interdisciplinary Investigation, Protein Identification, Tandem Mass Spectra

• Type: Conference
• Year: 2009
• Where: SIGIR
• Authors: Yiming Yang, Subramaniam Ganapathy, Abhay Harpale
• Keywords: Information Retrieval, Popular Ir Approaches, Protein Identification, SIGIR 2009, Tandem Mass Spectra