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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...

Tandem Mass Spectrometry

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...

MALDI-TOF Mass Spectrometry

MALDI-TOF Mass Spectrometry

Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...

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Related Experiment Video

Updated: Jul 15, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Novel peptide identification from tandem mass spectra using ESTs and sequence database compression.

Nathan J Edwards¹

¹Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. nedwards@umiacs.umd.edu

Molecular Systems Biology

|April 18, 2007

Summary

This study introduces a novel method for peptide identification in proteomics by searching expressed sequence tags (ESTs). This approach enhances protein isoform discovery, overcoming limitations of traditional protein sequence databases.

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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

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Published on: March 23, 2020

Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Tandem mass spectrometry is the primary method for peptide identification in proteomics.
Current search engines rely on protein sequence databases, failing to identify peptides from alternative splicing and coding SNP protein isoforms.

Framework:

Proposes searching expressed sequence tags (ESTs) for enhanced peptide identification.
Addresses computational infeasibility of large EST databases through sophisticated compression strategies.

Implementation:

Developed a sequence database compression strategy reducing human EST database size approximately 35-fold.
Compressed EST database achieves size comparable to standard protein sequence databases, enabling routine searching.

Implications:

Facilitates discovery of novel peptides, particularly from uncharacterized protein isoforms.
Improves comprehensive protein characterization in complex biological samples.
Advances proteomics research by enabling identification of previously missed peptide sequences.