An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics.

ABSTRACT:

Motivation

Cross-linking tandem mass spectrometry (XL-MS/MS) is an established analytical platform used to determine distance constraints between residues within a protein or from physically interacting proteins, thus improving our understanding of protein structure and function. To aid biological discovery with XL-MS/MS, it is essential that pairs of chemically linked peptides be accurately identified, a process that requires: (i) database search, that creates a ranked list of candidate peptide pairs for each experimental spectrum and (ii) false discovery rate (FDR) estimation, that determines the probability of a false match in a group of top-ranked peptide pairs with scores above a given threshold. Currently, the only available FDR estimation mechanism in XL-MS/MS is the target-

SUBMITTER: Peng Y 

PROVIDER: S-EPMC11256928 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature