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Comparison of database search strategies for high precursor mass accuracy MS/MS data
Edward J Hsieh1, Michael R Hoopmann, Brendan MacLean
1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Journal of Proteome Research
|November 27, 2009
Summary
High mass accuracy in shotgun proteomics improves peptide identification. Searching spectra with a wide mass tolerance and using precursor mass as a filter enhances accuracy, while narrow windows speed up searches but reduce identifications.
Area of Science:
- Proteomics
- Mass Spectrometry
- Bioinformatics
Background:
- Shotgun proteomics relies on tandem mass spectrometry for peptide identification.
- High mass accuracy measurements are crucial for improving data analysis.
- Existing database search strategies require evaluation for optimal performance.
Purpose of the Study:
- To evaluate two database search strategies utilizing high mass accuracy precursor ion measurements in shotgun proteomics.
- To determine the impact of mass tolerance windows on peptide identification rates and search times.
Main Methods:
- Analysis of tandem mass spectrometry data from peptides.
- Implementation and comparison of two database search strategies.
- Utilizing high mass accuracy measurements of peptide precursor ions.
- Varying mass tolerance windows (wide vs. narrow) for database searches.
Main Results:
- Peptide identifications are significantly improved when spectra are searched with a wide mass tolerance window.
- Using precursor mass as a filter effectively discards incorrect peptide matches.
- Constraining database searches to a narrow mass window reduces the number of peptide identifications.
- Narrow mass window searches result in significantly faster database search times.
Conclusions:
- High mass accuracy data, when combined with appropriate search parameters, enhances peptide identification in shotgun proteomics.
- A wide mass tolerance window coupled with precursor mass filtering is recommended for maximizing peptide identification accuracy.
- Narrow mass windows offer a trade-off between speed and the number of identifications, suitable for specific applications.
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