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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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Resin-Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation

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Comparative informatics analysis to evaluate site-specific protein oxidation in multidimensional LC-MS/MS data.

Carlee S McClintock¹, Jerry M Parks, Marshall Bern

¹Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, Tennessee 37830, USA.

Journal of Proteome Research

|July 6, 2013

Summary

This study advances redox proteomics by developing methods to detect low-abundance oxidized peptides. Enhanced sensitivity reveals surprising oxidation patterns on less reactive amino acid residues, improving disease insight.

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Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Published on: April 4, 2018

Area of Science:

Proteomics
Biochemistry
Mass Spectrometry

Background:

Redox proteomics offers insights into diseases linked to oxidative stress.
Detecting protein oxidation products is crucial for understanding these diseases.
Hydroxyl radical-based oxidative footprinting provides structural information but presents analytical challenges.

Purpose of the Study:

To develop robust methods for detecting oxidized peptides, especially those at low abundance.
To identify prevalent oxidized residues and their distribution on proteins.
To improve the interpretation of mass spectral data in redox proteomics.

Main Methods:

Electrochemical oxidation of model proteins.
Analysis at both intact protein and peptide levels.
Multidimensional chromatography to enhance dynamic range.
Hybrid database searching software (Inspect, Byonic) with de novo interpretation.

Main Results:

Identification of a prevailing set of oxidized residues.
Evaluation of oxidation sites informed by molecular dynamics simulations of solvent accessibility.
Discovery of unexpected oxidation on less reactive amino acid residues, in addition to known hotspots.
Enhanced sensitivity enabled detection of low-abundance oxidized peptides.

Conclusions:

The developed methods improve the detection of oxidized peptides, even those at low abundance.
This approach reveals novel insights into oxidative stress mechanisms by identifying oxidation sites on less reactive residues.
Findings contribute to a better understanding of protein dysfunction in diseases related to oxidative stress.