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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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Related Experiment Video

Updated: Apr 20, 2026

Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling

Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling

Published on: July 1, 2014

Peptide separation methodologies for in-depth proteomics.

Sajad Majeed Zargar¹, Rie Kurata, Randeep Rakwal

¹Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan.

Methods in Molecular Biology (Clifton, N.J.)

|November 20, 2014

Summary

This summary is machine-generated.

Identifying low-abundance proteins is crucial for comprehensive cell analysis. This study details gel-free mass spectrometry methods for enhanced protein identification in Arabidopsis thaliana.

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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Area of Science:

Proteomics
Biochemistry
Molecular Biology

Background:

Proteomics integration with other omics requires comprehensive protein identification and quantification.
Traditional 2-D gel electrophoresis has limitations, including time, skill requirements, and inability to detect low-abundance proteins masked by high-abundance ones.

Purpose of the Study:

To describe methods for extracting microsomal proteins and performing mass spectrometry (MS) analysis.
To focus on identifying low-abundance proteins using gel-free MS approaches in Arabidopsis thaliana.

Main Methods:

Microsomal protein extraction from Arabidopsis thaliana.
Application of three gel-free mass spectrometry-based methods: OFFGEL fractionation, 2D-LC, and a long-column method.
Peptide separation and MS analysis for low-abundance protein identification.

Main Results:

Detailed protocols for low-abundance protein identification using gel-free MS techniques.
Demonstration of effective peptide separation for in-depth proteomics.

Conclusions:

Gel-free mass spectrometry approaches are essential for identifying low-abundance proteins, overcoming limitations of traditional methods.
This work facilitates in-depth proteomics investigations for understanding cellular regulatory networks.