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Related Experiment Video

Updated: Dec 4, 2025

PIPEMAT-RS: Development and Validation of a Standardized MATLAB Pipeline for Resting-State EEG Preprocessing

PIPEMAT-RS: Development and Validation of a Standardized MATLAB Pipeline for Resting-State EEG Preprocessing

Published on: June 6, 2025

QuantPipe: A User-Friendly Pipeline Software Tool for DIA Data Analysis Based on the OpenSWATH-PyProphet-TRIC

Dazheng Wang¹, Guohong Gan¹, Xi Chen^2,3

¹State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University, Xiamen, P. R. China.

Journal of Proteome Research

|October 22, 2020

Summary

QuantPipe is a new graphical software tool that simplifies data-independent acquisition mass spectrometry analysis. It enhances the OpenSWATH-PyProphet-TRIC workflow, making complex data analysis more accessible for researchers.

Keywords:

OpenSWATH SWATH-MS data-independent acquisition diaPASEF

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Published on: June 5, 2021

Area of Science:

Proteomics
Mass Spectrometry
Bioinformatics

Background:

Data-independent acquisition (DIA) mass spectrometry is crucial for quantitative proteomics.
Analyzing DIA data typically requires command-line execution of complex workflows like OpenSWATH-PyProphet-TRIC.
There is a need for user-friendly software to streamline DIA data analysis.

Purpose of the Study:

To develop QuantPipe, a graphical user interface (GUI) software for DIA mass spectrometry data analysis.
To provide an accessible alternative to command-line based DIA analysis workflows.
To enhance the functionality of the OpenSWATH-PyProphet-TRIC workflow.

Main Methods:

Developed QuantPipe as a GUI based on the OpenSWATH-PyProphet-TRIC workflow.
Integrated functionalities for spectral library to assay library conversion.
Enabled output of peptide and protein intensities.

Main Results:

QuantPipe successfully analyzed various DIA-MS datasets, including SWATH-MS (TripleTOF 5600/6600), phospho-SWATH-MS, Orbitrap DIA, and TimsTOF Pro diaPASEF.
The software provides a user-friendly interface for complex mass spectrometry data analysis.
QuantPipe offers enhanced capabilities beyond the standard OpenSWATH-PyProphet-TRIC workflow.

Conclusions:

QuantPipe offers a powerful and accessible GUI for DIA mass spectrometry data analysis.
The software supports a wide range of DIA instruments and data types.
QuantPipe democratizes advanced proteomics data analysis through its user-friendly design and open accessibility.