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OJBTM
Online Journal of Bioinformatics ©
Volume
6 (2) 174-183, 2005
Boosting Speed of MS/MS Peptide Sequencing via
Database Search by Spectral Profile Comparison
Liu J, Carrillo B, Yanofsky C, Beaudrie C, Morales
F,
Department of Biomedical Engineering,
ABSTRACT
Liu J, Carrillo B, Yanofsky
C, Beaudrie C, Morales F, Kearney R, Boosting Speed
of MS/MS Peptide Sequencing via Database Search by Spectral Profile Comparison, Online J Bioinformatics 2 (6)
174-183, 2005. In
proteomics, tandem mass spectrometry is the key technology for peptide
sequencing. The analysis of MS/MS spectra is not always straight due to
problems such as noise and missing ions. Many sophisticated methods have been
proposed to sequence peptides through tandem mass spectra. While the solutions
are capable of providing more robust and accurate results, they are also
computationally expensive, creating a bottleneck in high throughput peptide
identification. In this work, we introduce a novel method to accelerate speed
of peptide sequencing. In contrast to existing approaches, we first conduct a
coarse comparison of spectral profiles to drastically shrink the number of
candidate peptides. A fast algorithm has been developed to achieve this goal.
We show that this approach can significantly improve the speed of peptide
sequencing with little damage on the accuracy. Since this approach can be used
as an independent preprocessing step, it can be readily coupled with other
database search programs for MS/MS analysis
Keywords: proteomics, tandem
mass spectrometry, peptide sequencing, database search.