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Peptide Identification Using Tandem Mass Spectrometry

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Updated: Jun 8, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Instrumentation for LC-MS/MS in proteomics.

Robert Chalkley¹

¹Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA.

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

|September 15, 2010

Summary

Modern mass spectrometers enable rapid analysis of complex proteomic samples. This chapter explores instrument options for protein and peptide analysis, detailing their strengths for identification, modification characterization, and quantitative measurements.

Area of Science:

Proteomics
Analytical Chemistry
Biochemistry

Background:

Advancements in mass spectrometry sensitivity and acquisition rates enable high-throughput analysis of complex biological samples.
Chromatographic separation coupled with mass spectrometry is crucial for analyzing proteomic samples.

Purpose of the Study:

To present various mass spectrometry instrument options for protein and peptide analysis.
To compare the strengths and weaknesses of different instruments for specific proteomic applications.

Main Methods:

Review of mass spectrometry instrumentation relevant to proteomics.
Discussion of analytical capabilities including protein identification, post-translational modification characterization, and quantitative analysis.

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A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

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Main Results:

Mass spectrometers offer sufficient sensitivity and speed for proteomic analysis on a chromatographic timescale.
Different instrument platforms provide distinct advantages for various proteomic data outputs.

Conclusions:

The selection of mass spectrometry instrumentation is critical for achieving specific proteomic analysis goals.
Understanding instrument capabilities facilitates informed choices for protein and peptide characterization in complex samples.