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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 Spectrum: Interpretation

Mass Spectrum: Interpretation

An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...

Chemical Ionization (CI) Mass Spectrometry

Chemical Ionization (CI) Mass Spectrometry

The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...

Mass Spectrum

Mass Spectrum

A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...

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Related Experiment Video

Updated: May 9, 2026

Determination of the Gas-phase Acidities of Oligopeptides

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities.

Brian A Risk¹, Nathan J Edwards, Morgan C Giddings

¹Department of Biochemistry & Biophysics, UNC School of Medicine, Chapel Hill, North Carolina 27599, United States. brian@geneffects.com

Journal of Proteome Research

|July 24, 2013

Summary

Peppy, a novel proteogenomic and proteomic search software, offers improved accuracy in peptide identification. Its unique scoring system enhances confidence scores for better false discovery rate estimation.

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Determination of the Gas-phase Acidities of Oligopeptides

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Published on: January 20, 2022

Area of Science:

Proteogenomics
Proteomics
Bioinformatics

Background:

Accurate peptide identification is crucial in mass spectrometry-based proteomics.
Existing scoring systems may have limitations in assessing spectral match quality.

Purpose of the Study:

To introduce Peppy, a novel software for proteogenomic and proteomic analysis.
To present a new scoring method for evaluating MS/MS spectrum and peptide sequence matches.
To compare Peppy's performance against other established search engines.

Main Methods:

Developed a scoring system using three binomial probability-based factors.
Calculated probabilities for random fragment ion alignment, peak intensity selection, and y-ion vs. b-ion intensity ratios.
Integrated Peppy into the PepArML meta-search engine for comparative analysis.

Main Results:

Peppy's scoring system provides global confidence scores for accurate comparisons and false discovery rate estimation.
In comparative analyses using PepArML, Peppy demonstrated superior accuracy on two out of four datasets.
Peppy was compared against Mascot, MSGF+, OMSSA, X!Tandem, k-Score, and s-Score.

Conclusions:

Peppy offers a novel and accurate approach to peptide identification in proteogenomic and proteomic studies.
The developed scoring method enhances the reliability of mass spectrometry data analysis.
Peppy is available as a downloadable software for researchers.