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bioRxiv · 10.1101/2024.10.11.617953

Comet fragment-ion indexing for enhanced peptide sequencing

McGann, C. D.·Bergstrom, E. J.·Sharma, V.·Heil, L. R.·Yu, Q.·Eng, J. K.·Schweppe, D. K.
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Abstract

Fragment ion indexing has significantly improved the efficiency of proteomics database search tools. This work implements fragment ion indexing in Comet, a widely-used, open-source search engine. We demonstrate that this enhancement maintains scoring and identification accuracy while substantially increasing peptide spectral matching speeds across multiple applications, including open modification searches, immunopeptidomics, and real-time searches. Comet-FI reduced search speeds by up to 94%, enabling the rapid analysis of complex data types like immunopeptidomes. Fragment-ion indexing enables Comet to keep pace with modern instrumentation and expanding applications in proteomics, reinforcing its utility in diverse proteomics workflows and its integration with a wide range of proteomics tools and platforms.

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McGann, C. D., Bergstrom, E. J., Sharma, V., Heil, L. R., Yu, Q., Eng, J. K., Schweppe, D. K.. 2024-10-15. Comet fragment-ion indexing for enhanced peptide sequencing. https://doi.org/10.1101/2024.10.11.617953

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