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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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Related Experiment Video

Updated: Sep 24, 2025

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain

Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain

Published on: April 28, 2022

Tandem Mass Spectrometry-Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing.

William S Phipps¹, Kelly D Smith^1,2, Han-Yin Yang³

¹Department of Laboratory Medicine and Pathology, Seattle, WA, USA.

American Journal of Clinical Pathology

|May 5, 2022

Summary

This summary is machine-generated.

Simplified amyloid typing using mass spectrometry is now accessible. Manual tissue sampling and the Crux Pipeline enable accurate amyloidosis diagnosis in clinical settings.

Keywords:

Amyloid Crux Liquid chromatography Open source Tandem mass spectrometry

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Published on: February 12, 2015

Area of Science:

Biochemistry
Proteomics
Clinical Diagnostics

Background:

Standard amyloid typing via liquid chromatography-tandem mass spectrometry (LC-MS/MS) requires specialized equipment, limiting clinical accessibility.
There is a need for simplified, cost-effective methods for amyloid typing in routine laboratory settings.

Purpose of the Study:

To develop and validate accessible methods for amyloid typing using LC-MS/MS.
To improve the ease of tissue sampling and data processing for amyloidosis diagnosis.

Main Methods:

Validated a manual tissue sampling technique as an alternative to laser microdissection.
Developed Crux Pipeline, an open-source workflow for automated data processing, including peptide identification and label-free quantification.
Incorporated a semiquantitative measure for assessing sampling adequacy.

Main Results:

Achieved 100% specificity in distinguishing major amyloidosis types using protein measurements and kappa/lambda light chain ratios.
Demonstrated the efficiency of Crux Pipeline for rapid, batched processing of mass spectrometry data.
Confirmed the utility of manual sampling combined with Crux Pipeline for accurate amyloid typing.

Conclusions:

Mass spectrometry-based amyloid typing is feasible without laser microdissection, enhancing accessibility.
Manual sampling and the Crux Pipeline provide a practical entry point into solid tissue proteomics for clinical laboratories.
These advancements facilitate broader adoption of mass spectrometry for diagnosing amyloidosis.