CapsPASEF – Collisional Cross Section Assisted Precursor Selection Applied to Cross-linking Mass Spectrometry

ABSTRACT: Ion mobility separates molecules in the gas-phase on their physico-chemical properties, providing information about their size as collisional cross-sections. The timsTOF Pro combines trapped ion mobility with a quadrupole, HCD cell and a time-of-flight mass spectrometer, to interrogate ions at high speeds with on-the-fly fragmentation. Ion mobility is perfectly suited for cross-linking mass spectrometry, which aims to uncover spatial restraints for proteins. The used cross-linking reagents covalently link amino acids in close proximity, resulting in peptide pairs after proteolytic digestion. This technique however suffers in terms of the low abundance of cross-linked peptides, which is partially resolved with enrichable cross-linking reagents. This class of reagents enables selective enrichment of cross-linking reagent modified peptides, resulting in selection of the cross-linked peptide pairs and peptides connected to a partially hydrolyzed reagent – termed mono-links. Even though mono-links carry limited structural information, for experiments aiming to uncover protein interactions in an unbiased manner they are unwanted byproducts. Gas-phase separation by IM has the potential to separate the two products and, indeed, we find separation between mono-links and cross-linked peptide pairs for PhoX cross-linked proteins. Moreover, an easy-to-interpret division at a CCS of 500 Å and a mono-isotopic mass of 2 kDa is present, which can be used for precursor selection. From our experiments on low complexity protein systems, sequencing of 50 - 70% of the mono-links is prevented, allowing the mass spectrometer the focus on sequencing the relevant cross-links. Application to a highly complex lysate focusing provides a 10-50 % increase in detected cross-links.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human) Bos Taurus (bovine)

SUBMITTER: Richard Scheltema  

LAB HEAD: Richard Alexander Scheltema

PROVIDER: PXD018189 | Pride | 2020-07-22

REPOSITORIES: Pride