Open Benchmark Dataset for Enzymatic Q–K Crosslink Identification by LC–MS/MS

This repository contains two LC–MS/MS raw data files (and .mgf versions if needed), associated search parameters, and curated FASTA databases generated from purified fibrinogen clots crosslinked by endogenous FXIIIa or recombinant transglutaminase 2 (TG2). These samples represent a controlled benchmark system for evaluating crosslink-mass spectrometry (XL-MS) software performance on non-cleavable enzymatic Q–K isopeptide bonds. Unlike conventional chemical crosslinkers, these transglutaminase-mediated crosslinks are zero-length modifications formed by ammonia (NH₃) loss, creating unique challenges for false discovery control and site assignment. The datasets are provided to enable transparent, community-driven comparison of XL search engines and to advance methodological development in enzymatic crosslink identification.