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Discovering known and unanticipated protein modifications using MS/MS database searching.
Wilfred H Tang1, Benjamin R Halpern, Ignat V Shilov
1Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA. tangwh@ appliedbiosystems.com
Analytical Chemistry
|July 1, 2005
Summary
This study introduces a faster MS/MS database search algorithm for identifying protein modifications. The new method significantly increases the number of identified MS/MS scans, revealing unexpected biological insights.
Area of Science:
- Proteomics
- Bioinformatics
- Mass Spectrometry
Background:
- Accurate identification of protein modifications is crucial for understanding biological processes.
- Traditional database search algorithms face limitations in speed and comprehensive modification detection.
Purpose of the Study:
- To develop a novel MS/MS database search algorithm for rapid and comprehensive protein modification discovery.
- To enhance the identification rate of MS/MS scans by accommodating known and unanticipated modifications.
Main Methods:
- Implementation of a novel protein database structure with extensive preindexing.
- Development of zone modification searching for known and unanticipated delta masses.
- Integration of these features into the Interrogator search engine.
Main Results:
- The modification-tolerant algorithm is 100-fold faster than traditional methods for comprehensive searches.
- A significant increase in identified MS/MS scans, with 158 out of 473 scans corresponding to modified peptides.
- Discovery of unexpected modifications, amino acid mutations, and artifacts from sample handling.
Conclusions:
- The developed algorithm enables rapid and broad discovery of protein modifications.
- This advancement significantly improves the percentage of identifiable MS/MS scans.
- Facilitates the discovery of biologically significant and unexpected modifications and sample-related artifacts.