Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package

Area of Science:

• Proteomics
• Mass Spectrometry
• Bioinformatics

Background:

• Ion mobility mass spectrometry (IM-MS) is increasingly utilized in proteomics.
• Bruker timsTOF instruments generate large datasets requiring specialized software for analysis.
• The open release of the timsTOF data format by Bruker enables community-driven software development.

Purpose of the Study:

• To develop the first Free Open Source Software (FOSS) solution for native timsTOF data processing.
• To create an integrated software environment for quantitative proteomics analysis of timsTOF data.
• To introduce i2MassChroQ, a software tool for peptide identification, protein inference, and quantification.

Main Methods:

• Development of i2MassChroQ, a FOSS software package.
• Native reading and low-level processing of timsTOF data.
• Benchmarking i2MassChroQ against existing proteomics software.

Main Results:

• i2MassChroQ demonstrated superior feature extraction capabilities.
• The software achieved a wider protein quantitative dynamic range.
• Improved protein quantification was observed in both technical replicates and differential abundance analyses.

Conclusions:

• i2MassChroQ provides a powerful FOSS solution for timsTOF data analysis in proteomics.
• The software enhances the efficiency and scope of quantitative proteomics studies.
• This development facilitates broader access to advanced proteomics data processing capabilities.