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. 2020 Nov 25;19(10):1677–1687. doi: 10.1074/mcp.RA120.002094

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© 2020 © 2020 Steigenberger et al.

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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Fig. 2 — Collisional Cross Section Assisted Precursor Selection (caps-PASEF) applied to cross-linked BSA.A, Identical to Fig. 1; distribution of m/z (Th) versus CCS for all classes of ions, converted to B, monoisotopic mass versus CCS. The red dotted polygon contains most of the cross-linked peptides. C, Overview of the classes of ions in- and outside the defined polygon area; (grey: unidentified, red: cross-links, blue:monolinks) D, Data collected in optimized caps-PASEF mode (Unidentified: likely noise; Mono-link: 30; Cross-link: 98). E, Comparison of mono-link and cross-link identification results in PASEF and caps-PASEF mode. The ratio cross-linked versus mono-linked peptides increases from 0.4:1 to 3.2:1 going from PASEF to caps-PASEF mode.