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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.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Updated: Jun 16, 2025

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

Racetrack FAIMS for High-Resolution and High-Sensitivity Characterization of Peptide Conformers.

Junhui Li^1,2,3, Rong Liu^1,2,3, Zhonghan Hu^1,2,3

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

Analytical Chemistry

|August 17, 2024

Summary

A new racetrack field asymmetric waveform ion mobility spectrometry (r-FAIMS) device offers significantly improved sensitivity and resolution for peptide analysis. This advanced instrument enhances the exploration of biomolecular conformational diversity with greater precision.

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Area of Science:

Analytical Chemistry
Biophysical Chemistry
Spectrometry

Background:

Ion mobility spectrometry (IMS) is crucial for analyzing biomolecular structures.
Existing planar FAIMS (p-FAIMS) offers good resolution but can be limited in sensitivity.
Exploring peptide conformational diversity requires high-resolution and high-sensitivity analytical techniques.

Purpose of the Study:

To develop and evaluate a novel racetrack field asymmetric waveform ion mobility spectrometry (r-FAIMS) device.
To compare the performance of r-FAIMS against traditional planar FAIMS (p-FAIMS).
To assess the capability of r-FAIMS for high-resolution and high-sensitivity analysis of peptide conformational diversity.

Main Methods:

Development of a hybrid cylindrical and planar FAIMS device (r-FAIMS) with a 1 mm gap width.
Systematic optimization of r-FAIMS operating conditions using pure nitrogen as carrier gas.
Comparative analysis of r-FAIMS and p-FAIMS performance using bradykinin and syntide 2 ions.

Main Results:

r-FAIMS demonstrated an ~8.5-fold increase in spectral intensity compared to p-FAIMS for doubly charged bradykinin ions, indicating superior sensitivity.
r-FAIMS achieved ~1.70-fold higher peak separation resolution than p-FAIMS under similar sensitivity conditions.
r-FAIMS achieved a resolving power exceeding 120 for triply charged syntide 2 ions, significantly outperforming p-FAIMS (44.2 resolving power).

Conclusions:

The developed r-FAIMS device significantly enhances both sensitivity and resolution in ion mobility spectrometry.
r-FAIMS enables more effective structural characterization of biomolecules, particularly for exploring peptide conformational diversity.
The novel r-FAIMS design offers a substantial advancement for high-performance analytical applications in chemistry and biology.