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Updated: Jul 4, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
Published on: October 15, 2018
Automated gain control ion funnel trap for orthogonal time-of-flight mass spectrometry
Yehia M Ibrahim1, Mikhail E Belov, Andrei V Liyu
1Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
Abstract:
Time-of-flight mass spectrometry (TOF MS) is increasingly used in proteomics research. Herein, we report on the development and characterization of a TOF MS instrument with improved sensitivity equipped with an electrodynamic ion funnel trap (IFT) that employs an automated gain control (AGC) capability. The IFT-TOF MS was coupled to a reversed-phase capillary liquid chromatography (RPLC) separation and evaluated in experiments with complex proteolytic digests. When applied to a global tryptic digest of Shewanella oneidensis proteins, an order-of-magnitude increase in sensitivity compared to that of the conventional continuous mode of operation was achieved due to efficient ion accumulation prior to TOF MS analysis. As a result of this sensitivity improvement and related improvement in mass measurement accuracy, the number of unique peptides identified in the AGC-IFT mode was 5-fold greater than that obtained in the continuous mode.
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