Cross-linking/mass spectrometry has evolved into a robust technology that reveals structural insights into proteins and protein complexes. We leverage a new tribrid instrument with improved fragmentation capacities in a systematic comparison to identify Which fragmentation method would be best for the identification of cross-linked peptides. Specifically, we explored three fragmentation methods and two combinations: collision -induced dissociation (CID), beam -type CID (HCD), electron -transfer -dissociation (ETD), ETciD, and EThcD. Trypsin-digested, SDA-cross-linked human serum albumin (HSA) served as a test sample, yielding, over all methods and in triplicate analysis in total 2602 matched PSMs and 1390 linked residue pairs at 5% false discovery rate, as confirmed by the crystal structure. HCD wins in number of matched peptide-spectrum-matches (958 PSMs) and identified links (446). 'CID is most completrientaty, increasing the number of identified links by 13% (58 links). HCD wins together with EThcD in cross-link site calling preciSion, with approximately 62% of sites having adjacent backbone cleavages that unambiguously locate the link in both peptides, without assuming.any cross-linker preference for amino acids. Overall quality of spectra, as judged by sequence coverage of both peptides, is best for EThcD for the majority of peptides. Sequence coverage might-be:of particular importance for complex samples, for Which we propose a data dependent decision tree,, else HCD is the method of choice. The mass spectrometric-taw data has been deposited in PRIDE (PXDO03737).
展开▼
