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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, Kearney R.

 

Department of Biomedical Engineering, McGill University, Montreal Quebec, Canada.

 

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. Onl J Bioinform., 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.


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