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Published on: May 9, 2017
Performance evaluation of existing de novo sequencing algorithms
Sergey Pevtsov1, Irina Fedulova, Hamid Mirzaei
1Department of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Moscow 119992.
Journal of Proteome Research
|November 4, 2006
Summary
We evaluated five de novo sequencing algorithms for protein identification from mass spectrometry data. PEAKS and NovoHMM generally performed best, with performance varying by instrument type.
Area of Science:
- Proteomics
- Bioinformatics
- Mass Spectrometry
Background:
- Protein identification from tandem mass spectra is crucial in proteomics.
- Two primary methods exist: database searching and de novo sequencing.
- De novo sequencing directly determines peptide sequences from spectra.
Purpose of the Study:
- To evaluate and compare the performance of five de novo sequencing algorithms: AUDENS, Lutefisk, NovoHMM, PepNovo, and PEAKS.
- To assess algorithm performance based on relative sequence distance (RSD), sensitivity, and spectrum quality.
- To determine how algorithm performance varies between QSTAR and LCQ mass spectrometer data.
Main Methods:
- Comparative analysis of five de novo sequencing algorithms.
- Performance metrics included relative sequence distance (RSD), sensitivity, and spectrum quality.
- Data analyzed from QSTAR and LCQ mass spectrometers.
Main Results:
- Algorithm performance differed between QSTAR and LCQ data; generally better on QSTAR.
- For QSTAR data: PEAKS > Lutefisk, PepNovo > AUDENS, NovoHMM. PEAKS showed best sensitivity and performance across spectrum qualities.
- For LCQ data: NovoHMM > PepNovo, PEAKS > Lutefisk > AUDENS. NovoHMM exhibited best sensitivity and overall performance.
Conclusions:
- PEAKS and NovoHMM are top-performing de novo sequencing algorithms, with PEAKS excelling on QSTAR and NovoHMM on LCQ.
- Algorithm choice impacts protein identification accuracy and depends on the mass spectrometer used.
- AUDENS and NovoHMM showed less sensitivity to spectrum quality variations compared to PEAKS, Lutefisk, and PepNovo.
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