DMDSSO Cross-Linked Peptide Analysis

DMDSSO cross-linked peptides were analysed by LC-MSⁿ utilizing an LTQ-Orbitrap XL MS (Thermo Fisher, San Jose, CA) coupled on-line with an Easy-nLC 1,000 (Thermo Fisher, San Jose, CA) as previously described29 (link)31 (link). Each MSⁿ experiment consists of one MS scan in FT mode (350–1,400 m/z, resolution of 60,000 at m/z 400) followed by two data-dependent MS2 scans in FT mode (resolution of 7,500) with normalized collision energy at 20% on the top two MS peaks with charges at 3+ or up, and three MS3 scans in the LTQ with normalized collision energy at 35% on the top three peaks from each MS2.

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Yu C., Mao H., Novitsky E.J., Tang X., Rychnovsky S.D., Zheng N, & Huang L. (2015). Gln40 deamidation blocks structural reconfiguration and activation of SCF ubiquitin ligase complex by Nedd8. Nature Communications, 6, 10053.

Publication 2015

LTQ-Orbitrap XL MS Easy-nLC 1,000

Line 1 Peptides Scans

Corresponding Organization :

Other organizations : University of California, Irvine, Howard Hughes Medical Institute, University of Washington

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Variable analysis

independent variables

LC-MSⁿ analysis
LTQ-Orbitrap XL MS
Easy-nLC 1,000

dependent variables

DMDSSO cross-linked peptides

control variables

Collision energy (20% for MS2, 35% for MS3)
Scan parameters (350–1,400 m/z, resolution of 60,000 at m/z 400 for MS1, resolution of 7,500 for MS2)

controls

No positive or negative controls were explicitly mentioned.

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