Proteomics

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Expanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS


ABSTRACT: In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here we present a gas-phase separation strategy using high field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to the Orbitrap Tribrid mass spectrometers. By enabling an additional peptide separation step in gas phase using the FAIMS device, we increase the number of cross-link identification by 22% for a medium complex sample and 59% for strong cation exchange-fractionated HEK293T cell lysate in XL-MS experiments using disuccinimidyl sulfoxide (DSSO) cross-linker. When disuccinimidyl suberate (DSS) cross-linker is in use, we are able to boost cross-link identification by 89% for the medium and 100% for the highly complex sample comparing to the analyses without FAIMS . Furthermore, we show that for medium complex samples, FAIMS enables the collection of single-shot XL-MS data with comparable depth to the corresponding sample fractionated by chromatography-based approaches. Altogether, we demonstrate FAIMS is highly beneficial for XL-MS studies by expanding the proteome coverage of cross-links while improving the efficiency and confidence of cross-link identification.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Gallus gallus   Homo sapiens   Equus caballus   Bos taurus  

TISSUE(S): Tissue Not Applicable To Dataset, Cell Culture

DISEASE(S): Not Available

SUBMITTER: Lennart Schnirch  

LAB HEAD: Fan Liu

PROVIDER: PXD019926 | Pride | 2020-07-22

REPOSITORIES: pride

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Publications

Expanding the Depth and Sensitivity of Cross-Link Identification by Differential Ion Mobility Using High-Field Asymmetric Waveform Ion Mobility Spectrometry.

Schnirch Lennart L   Nadler-Holly Michal M   Siao Siang-Wun SW   Frese Christian K CK   Viner Rosa R   Liu Fan F  

Analytical chemistry 20200723 15


In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here, we present a gas-phase separation strategy using high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to the Orbitrap Tribrid mass spectrometers. By enabling an additional peptide separation step in the gas  ...[more]

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