Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing

peer-reviewed · IEEE/ACM Transactions on Computational Biology and Bioinformatics · 2019

peer-reviewed · IEEE/ACM Transactions on Computational Biology and Bioinformatics · 2019. Tiancong Wang et al. A scoring function plays a critical role in software for peptide identification with mass spectrometry. We…
Date 2019-01-01
Type peer-reviewed
Venue IEEE/ACM Transactions on Computational Biology and Bioinformatics
Publisher Institute of Electrical and Electronics Engineers (IEEE)
Contribution algorithm
DOI 10.1109/tcbb.2018.2864647
Citations (OpenAlex) 0
Venue 2-year citedness 2.33

Abstract

A scoring function plays a critical role in software for peptide identification with mass spectrometry. We present a general scoring feature that can be incorporated in the scoring functions of other peptide identification software. The scoring feature is based on the intensity ratios between two adjacent y-ions in the spectrum. A method is proposed to obtain the probability distributions of such ratios, and to calculate the scoring feature based on the distributions. To demonstrate the performance of the method, the new feature is incorporated with X!Tandem [1] , [2] and Novor [3] and significantly improved the database search and de novo sequencing performances on the testing data, respectively.

Authors

  1. Tiancong Wang · University of Waterloo
  2. Bin Ma · Rapid Novor Inc., University of Waterloo, University of Western Ontario, Western University

Methods and tools

  • Novor: Real-time decision-tree scoring

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