MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.

ABSTRACT: Cross-linking mass spectrometry has become a powerful tool for the identification of protein-protein interactions and for gaining insight into the structures of proteins. We previously published MS Annika, a cross-linking search engine which can accurately identify cross-linked peptides in MS2 spectra from a variety of different MS-cleavable cross-linkers. In this publication, we present MS Annika 2.0, an updated version implementing a new search algorithm that, in addition to MS2 level, only supports the processing of data from MS2-MS3-based approaches for the identification of peptides from MS3 spectra, and introduces a novel scoring function for peptides identified across multiple MS stages. Detected cross-links are validated by estimating the false discovery rate (FDR) using a target-d

SUBMITTER: Birklbauer MJ 

PROVIDER: S-EPMC10476269 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature