Protein identification as an information retrieval problem

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.

REFERENCES

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INDEX TERMS

Primary Classification:
  H. Information Systems
  H.4 INFORMATION SYSTEMS APPLICATIONS
      H.4.m Miscellaneous

Additional Classification:
  H. Information Systems
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.3 Information Search and Retrieval
          Subjects: Retrieval models

General Terms:
Algorithms, Design, Experimentation, Performance

Keywords:
interdisciplinary investigation, protein identification, tandem mass spectra, vector space models