A New Tag Index Scheme Enables Fast Peptide Retrieval for Protein Identification

Abstract

Sequence tag index in the field of computational proteomics can be used to facilitate faster open-search-based identification of modified peptides and in-depth analysis of mass spectrometry data. In protein-identification search engines, sequence tag index are playing a prominent role in recent ten years due to fast searching speed. However, in pursuit of less index space consumption, some protein search engines design excessively concise index schemes which lead to higher computational burden. We proposed a new tag index scheme named TIIP with a better balance between space and time complexity. TIIP has a unique two-level hierarchical index structure which allows rapid retrieval of all peptide sequences and their corresponding masses. Theoretically, the index space consumption of TIIP is not much higher compared to the typical tag index schemes, but the time complexity of sequence retrieval can be reduced to O(1), and practically, TIIP has about one million fold improvement in searching speed compared with brute force approach.