Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx.

ABSTRACT: Cross-linking combined with mass spectrometry (XL-MS) provides a wealth of information about the three-dimensional (3D) structure of proteins and their interactions. We introduce MaxLynx, a novel computational proteomics workflow for XL-MS integrated into the MaxQuant environment. It is applicable to noncleavable and MS-cleavable cross-linkers. For both, we have generalized the Andromeda peptide database search engine to efficiently identify cross-linked peptides. For noncleavable peptides, we implemented a novel dipeptide Andromeda score, which is the basis for a computationally efficient N-squared search engine. Additionally, partial scores summarize the evidence for the two constituents of the dipeptide individually. A posterior error probability (PEP) based on total and partial

SUBMITTER: Yılmaz S 

PROVIDER: S-EPMC8792900 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature