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Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Two-Dimensional FAIMS-TIMS Separation for Probing Structural Diversity of Peptides with Resolution Exceeding 6500.

Junhui Li^1,2,3, Xixuan Gu^1,2,3, Yongqi Lei^1,2,4

¹Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, P. R. China.

Analytical Chemistry

|October 21, 2025

Summary

A new two-dimensional ion separation platform combining racetrack field asymmetric waveform ion mobility spectrometry (r-FAIMS) and trapped ion mobility spectrometry (TIMS) significantly enhances the resolution of biomolecule conformers. This advanced technique reveals nearly 30 distinct conformers for bradykinin ions, greatly improving structural analysis capabilities.

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Published on: November 15, 2017

Area of Science:

Analytical Chemistry
Biophysical Chemistry
Spectrometry

Background:

Ion mobility spectrometry (IMS) separates ions based on size, shape, and charge.
Resolving the conformational diversity of biomolecules in the gas phase is crucial for understanding their function.
Existing IMS techniques have limitations in resolving complex mixtures of conformers.

Purpose of the Study:

To develop and validate a two-dimensional ion separation platform by coupling racetrack field asymmetric waveform ion mobility spectrometry (r-FAIMS) with trapped ion mobility spectrometry (TIMS).
To explore the conformational diversity of doubly charged bradykinin (BK+2H⁺)²⁺ ions using the developed platform.
To assess the orthogonality and combined resolving power of the r-FAIMS-TIMS platform for biomolecular structural elucidation.

Main Methods:

Coupling of high-sensitivity and high-resolution racetrack field asymmetric waveform ion mobility spectrometry (r-FAIMS) with trapped ion mobility spectrometry (TIMS).
Optimization of r-FAIMS parameters, including carrier gas (nitrogen) and dispersion voltage (2.6 kV).
Sequential analysis of compensation voltage (CV)-selected ions from r-FAIMS using TIMS.

Main Results:

r-FAIMS resolved six distinct conformers of (BK+2H⁺)²⁺ ions based on compensation voltage.
TIMS resolved four conformers, but the r-FAIMS-TIMS platform resolved nearly 30 conformers of (BK+2H⁺)²⁺ ions.
Demonstrated high orthogonality between r-FAIMS and TIMS separation dimensions.
Achieved a total resolving power exceeding 6500 for (BK+2H⁺)²⁺ ions, significantly enhancing structural analysis.

Conclusions:

The developed two-dimensional r-FAIMS-TIMS platform offers superior resolving power for gas-phase ion separation.
This platform is highly effective for detailed structural elucidation of large biomolecules by resolving numerous conformers.
The orthogonality of the two techniques maximizes separation efficiency, overcoming limitations of single-dimension methods.