Renaissance of reporter ions for proteomic-level cross-linking analysis unveils molecular basis of transcription-translation link in bacteria

摘要

A central challenge for detailed protein characterisations is the reliable detection of modified or cross-linked peptides. The identification of cross-linked peptides, for example, is often a struggle against great odds and yet provides large potential benefits for modelling proteins and their complexes. Cross-linked peptides typically contribute little to an LC-MS data set. However, their presence significantly increases database size, as peptide pair-wise combinations need to be considered. This leads to a high chance of random matches, resulting from a large but poor dataset being matched against a large database. Ideally, data of cross-linked or any other target peptide should be separated from data of unwanted peptides before the database search. Reporter ions constitute a general candidate for such data sorting.