Don’t Waste Time – Ensure Success in Your Cross-Linking Mass Spectrometry Experiments Before You Begin.

ABSTRACT: Cross-linking mass spectrometry (XL-MS) is becoming a more popular tool for researchers to turn towards for studying proteins and their complexes of interest especially in complex samples such as lysates or whole-cells. Studying a targeted proteins in a complex mixture can be difficult as data on other higher abundant proteins may dominate, leaving little information on complexes of interest. Although it is known that cross-linking favours proteins of higher abundances, it is yet unclear what it means to be “abundant” to expect good cross-linking data. In this paper, we show that proteins of interest should be at least in the top 20 % abundance range to expect more than one cross-link found per protein. Furthermore, we show that a classical bottom-up LC-MS/MS experiment and iBAQ analysis can help determine the abundance level of proteins and a simple method to follow their enrichment if necessary. We hope that this guideline can be a starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Bacteria Neisseria Meningitidis Serogroup C (strain 8013)

SUBMITTER: Lucienne Nouchikian  

LAB HEAD: Julia Chamot-Rooke

PROVIDER: PXD045792 | Pride | 2024-02-07

REPOSITORIES: Pride