MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search

J Proteome Res. 2023 Feb 3;22(2):462-470. doi: 10.1021/acs.jproteome.2c00658. Epub 2023 Jan 23.


Spectral library search can enable more sensitive peptide identification in tandem mass spectrometry experiments. However, its drawbacks are the limited availability of high-quality libraries and the added difficulty of creating decoy spectra for result validation. We describe MS Ana, a new spectral library search engine that enables high sensitivity peptide identification using either curated or predicted spectral libraries as well as robust false discovery control through its own decoy library generation algorithm. MS Ana identifies on average 36% more spectrum matches and 4% more proteins than database search in a benchmark test on single-shot human cell-line data. Further, we demonstrate the quality of the result validation with tests on synthetic peptide pools and show the importance of library selection through a comparison of library search performance with different configurations of publicly available human spectral libraries.

Keywords: bioinformatics; peptide identification; proteomics; spectral library search; tandem mass spectrometry.