To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis

ABSTRACT: Cross-linking mass spectrometry is a powerful method for structural analysis, yet how to choose cross-linkers-cleavable versus non-cleavable-remains a challenge. Here, we evaluate non-cleavable DSS against cleavable DSSO across a spectrum of sample complexities, from isolated protein complexes to bacterial lysates. DSS consistently yields more cross-link identifications than DSSO, but the gap narrows as sample complexity increases. This performance advantage of DSS is attributed to its longer and more flexible spacer arm, which interrogates a spatial volume >40% larger than that of DSSO. For both, identification sensitivity decreases as search space expands, but more so for DSS than DSSO. This is due to a slightly lower fragment ion coverage of DSS cross-links, not absence of signature

SUBMITTER: Yong Cao 

PROVIDER: S-SCDT-10_1038-S44320-026-00222-9 | biostudies-other |

REPOSITORIES: biostudies-other