A Two-way Parallel Searching for Peptide Identiflcation via Tandem Mass Spectrometry
peer-reviewed · Engineering letters · 2006
| Date | 2006-11-01 |
| Type | peer-reviewed |
| Venue | Engineering letters |
| Contribution | algorithm |
| Link | http://www.engineeringletters.com/issues_v13/issue_3/EL_13_3_15.pdf |
| Citations (OpenAlex) | 0 |
Abstract
De novo peptide sequencing that determines the amino acid sequence of a peptide via tandem mass spectrometry (MS/MS) has been increasingly used nowadays in proteomics for protein identiflcation. Current de novo methods generally employ a graph theory, which usually produces a large number of candidate sequences and causes heavy computational cost while trying to determine a sequence with less ambiguity. We present a novel de novo sequencing algorithm that greatly reduces the number of candidate sequences. By utilizing certain properties of b- and y-ion series in MS/MS spectrum, we propose a reliable two-way parallel searching algorithm to fllter out the peptide candidates that are further pruned by an intensity evidence based screening criterion. In addition, we deflne an adjusted value required to determine the end node positions for band y-ion series in the case of +2 charged precursor. Experimental results demonstrate the e‐ciency and potency of the proposed algorithm.
Methods and tools
- Two-way parallel searching de novo: A de novo algorithm that searches b and y ion series in parallel from both ends to cut the number of candidate sequences, then screens them by intensity evidence.