Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A comparative analysis of early postoperative outcomes of autologous pericranium versus high-density polypropylene in cranial duraplasty in a tertiary care center in Central India.

Chinese neurosurgical journal·2026

Same author

Artificial Intelligence for Prognostic Modelling and Adaptive Treatment Monitoring in Radiation Oncology.

Cureus·2026

Same author

Reconfigurable MIMO antenna for Sub-6 GHz 5G cognitive radio with machine learning based metaheuristic optimization.

Scientific reports·2026

Same author

Dose-Dependent Escitalopram-Induced Anejaculation and Anorgasmia: Rapid Reversal After Discontinuation and Bupropion Therapy.

American journal of therapeutics·2026

Same author

GLP-1 receptor agonists and clinical outcomes in adults with Crohn's disease and obesity: a propensity score-matched real-world cohort study.

Scientific reports·2026

Same author

T1Ρ and T2 Mapping Magnetic Resonance Imaging as Predictors of Cartilage Loss in Early Anterior Cruciate Ligament Injury.

Journal of orthopaedic case reports·2026

Search research articles

Related Experiment Video

Updated: Nov 6, 2025

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

Automated Workflow for Peptide-Level Quantitation from DIA/SWATH-MS Data.

Shubham Gupta^1,2, Hannes Röst^3,4

¹Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.

Methods in Molecular Biology (Clifton, N.J.)

|May 5, 2021

Summary

This study presents an open-source workflow for quantitative proteomics using data-independent acquisition (DIA). The method simplifies the analysis of complex spectral data, enabling accurate peptide quantification across multiple runs.

Keywords:

DIA DIAlignR Data-independent acquisition OpenSWATH Retention time alignment SWATH-MS pyProphet

More Related Videos

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Related Experiment Videos

Last Updated: Nov 6, 2025

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

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Area of Science:

Proteomics
Mass Spectrometry
Bioinformatics

Background:

Data-independent acquisition (DIA) is a mass spectrometry technique for comprehensive sample analysis.
Analyzing complex DIA data for accurate peptide quantification requires sophisticated bioinformatics workflows.
Existing workflows can be challenging to install and use, hindering broader adoption.

Purpose of the Study:

To develop and present an open-source, user-friendly workflow for quantitative proteomics using DIA.
To streamline the process of generating a quantitative matrix from multiple DIA mass spectrometry runs.
To improve accessibility and reproducibility of DIA data analysis.

Main Methods:

The workflow integrates OpenSWATH, pyProphet, and DIAlignR for data processing.
It utilizes an "assay library" containing peptide MS coordinates as prior information.
Docker-based containerization is employed for simplified installation and cross-platform compatibility.

Main Results:

The developed workflow successfully generates a quantitative matrix from multiple DIA runs.
The integration of specified software tools ensures robust peptide quantification.
Containerization facilitates easy deployment and use, reducing dependency issues.

Conclusions:

This open-source workflow provides an accessible and efficient solution for quantitative proteomics using DIA.
The method enhances the ability to analyze complex spectral data and obtain reliable peptide quantification.
The use of containerization promotes reproducibility and wider application of DIA-based quantitative proteomics.