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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...

Mass Spectrometry: Complex Analysis

Mass Spectrometry: Complex Analysis

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Related Experiment Video

Updated: Jul 15, 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

A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry

Hua Xu¹, Michael A Freitas

¹Department of Chemistry, the Ohio State University, Columbus 43210, OH, USA. xu.171@osu.edu <xu.171@osu.edu>

BMC Bioinformatics

|April 24, 2007

Summary

A new scoring model enhances peptide and protein identification in mass spectrometry proteomics by assessing match probabilities. This improves accuracy in high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments.

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

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Area of Science:

Proteomics
Mass Spectrometry
Biochemistry

Background:

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a key technique in proteomics.
Automation is crucial for high-throughput LC-MS/MS experiments.

Purpose of the Study:

To develop a statistical scoring model for peptide and protein identification in tandem mass spectrometry database searches.
To improve the accuracy and reliability of automated proteomics data analysis.

Main Methods:

Derivation of a probability-based statistical scoring model.
Assessment of peptide and protein matches using matched product ions and their abundance.
Incorporation of the algorithm into the MassMatrix automated database search program.

Main Results:

The model provides probability scores indicating the likelihood of a peptide match being a random occurrence.
Protein scores reflect the significance of matches, differentiating true from random identifications.
High mass accuracy improves scoring and reduces false positives.

Conclusions:

The developed scoring model enhances the accuracy of peptide and protein identification in LC-MS/MS.
The model implicitly accounts for mass accuracy, improving true positive scores and reducing false positives.
The algorithm is integrated into the MassMatrix software for automated database searching.