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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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Automated Sample Multiplexing by using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT

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Peptide ratios for post-mortem interval estimation using targeted liquid chromatography triple quadrupole mass

Jenna Ireland¹, Lana Brockbals^1,2, Dennis McNevin¹

¹Centre for Forensic Sciences, School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia.

International Journal of Legal Medicine

|December 25, 2025

Summary

This study optimized a targeted proteomics method for postmortem interval (PMI) estimation using muscle tissue. The developed liquid chromatography-triple quadrupole mass spectrometry (LC-QQQ) approach shows promise for routine forensic casework.

Keywords:

Analytical flow LC LC-MS/MS Muscle Post-mortem interval Proteomics Taphonomy Triple quadrupole mass spectrometry

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Area of Science:

Forensic Science
Biochemistry
Analytical Chemistry

Background:

Postmortem interval (PMI) estimation is crucial in forensic investigations but faces challenges, especially in later decomposition stages.
Current PMI methods have limitations; proteomics offers a more objective approach.
Previous research identified 19 peptide targets in muscle tissue correlated with decomposition time.

Purpose of the Study:

To optimize the detection of 19 previously identified peptide targets using a targeted liquid chromatography-triple quadruple mass spectrometry (LC-QQQ) method.
To assess the reproducibility and applicability of this targeted LC-QQQ method for forensic casework.
To conduct a longitudinal analysis of peptide targets in authentic human samples over 14 days postmortem.

Main Methods:

Development and optimization of a targeted LC-QQQ method for 19 specific peptide targets.
Analysis of human muscle tissue samples over a 14-day postmortem period.
Data analysis including generation of peptide ratios and log2 transformation.

Main Results:

17 out of 19 peptide targets were optimized for reproducible detection.
The targeted LC-QQQ method yielded interpretable results for most targets over the 14-day period.
Two previously proposed peptide ratios demonstrated linear trends after data transformation.

Conclusions:

A targeted LC-QQQ method is a viable system for detecting PMI peptide targets in human postmortem muscle tissue.
The optimized method shows potential for validation and application in routine forensic casework.
This proteomics-based approach offers a more objective tool for PMI estimation.