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Updated: Aug 12, 2026

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Published on: January 12, 2024
Improved Identification of Peptides, Modification Sites, and Cross-Link Sites by Target-Enhanced Accurate Inclusion
Adalet Memetimin1,2,3, Ching Tarn4,5, Peng-Zhi Mao4,5
1College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing100875, China.
Target-enhanced accurate inclusion mass screening (TAIMS) improves mass spectrometry sensitivity for identifying low-abundance cross-linked peptides and post-translational modifications, enhancing proteomic structural insights.
Area of Science:
- Proteomics
- Structural Biology
- Mass Spectrometry
Background:
- Chemical cross-linking coupled with mass spectrometry identifies protein structural features via cross-linked peptides.
- Current methods struggle with low sensitivity and MS2 quality for cross-links compared to linear peptides.
Purpose of the Study:
- To introduce and validate target-enhanced accurate inclusion mass screening (TAIMS) for improved cross-link identification.
- To demonstrate TAIMS's utility for low-abundance peptides and post-translational modifications.
Main Methods:
- Developed and optimized TAIMS, a targeted mass spectrometry approach.
- Applied TAIMS to yeast ribosome and E. coli lysate for cross-link analysis.
- Tested TAIMS on mouse brain samples for phosphopeptide identification.
Main Results:
- TAIMS significantly improved MS2 quality, increasing high-fragment ion coverage (FIC) cross-links by 359-678 (40% to ~90%).
- Enhanced cross-link site localization accuracy and mitigated sensitivity loss.
- Recovered previously unidentified cross-links and linear peptides, including 10 intermolecular cross-links missed by DDA.
- Increased phosphopeptide identification with accurate phosphosite assignment by 67% in mouse brain samples.
Conclusions:
- TAIMS substantially enhances sensitivity and accuracy in cross-link identification.
- TAIMS is a versatile method applicable to low-abundance peptides and post-translational modifications in proteomics.
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