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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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Updated: Jun 4, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Detecting Human Contaminant Genetically Variant Peptides in Nonhuman Samples.

Fanny Chu¹, Andy Lin¹

¹Chemical and Biological Signatures, Pacific Northwest National Laboratory, Seattle, Washington 98109, United States.

Journal of Proteome Research

|December 20, 2024

Summary

Human genetically variant peptides (GVPs) were detected in nonhuman proteomics data, suggesting they are common contaminants. These findings highlight the need to update standard contaminant databases for accurate mass spectrometry analysis.

Keywords:

contaminants forensic proteomics genetically variant peptides liquid chromatography-tandem mass spectrometry

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Area of Science:

Proteomics
Mass Spectrometry
Bioinformatics

Background:

Proteomics data analysis relies on searching experimental spectra against curated protein databases.
Standard databases often include organism proteomes and common contaminants like trypsin and keratins.
However, other contaminants may be present but are not routinely included in search databases.

Purpose of the Study:

To identify and characterize a novel set of protein contaminants in mass spectrometry-based proteomics data.
To provide evidence for the detection of human genetically variant peptides (GVPs) in nonhuman samples.
To assess the prevalence and origin of these GVPs in proteomics datasets.

Main Methods:

Reanalysis of previously collected nonhuman data-dependent acquisition (DDA) and data-independent acquisition (DIA) mass spectrometry datasets.
Identification of peptides containing single amino acid polymorphisms (human GVPs).
Statistical analysis to determine the likelihood of nonhuman origin for detected GVPs.

Main Results:

Between 0 and 135 human GVPs were detected per analyzed nonhuman dataset.
Evidence suggests that detected GVPs are unlikely to originate from nonhuman biological sources.
A common subset of eight GVPs was frequently detected across multiple datasets.

Conclusions:

Human GVPs represent a previously unrecognized class of contaminants in proteomics.
The routine detection of GVPs in nonhuman samples necessitates their inclusion in standard contaminant databases.
Updating search databases with GVPs will improve the accuracy and reliability of proteomics data interpretation.