multiFLEX-LF: A Computational Approach to Quantify the Modification Stoichiometries in Label-Free Proteomics Data...

Area of Science:

• Proteomics
• Computational Biology
• Biochemistry

Background:

• Protein modifications are crucial for cellular function but challenging to quantify using liquid chromatography-tandem mass spectrometry.
• Existing methods lack comprehensive analysis of modification presence and stoichiometry in large-scale proteomics data.

Purpose of the Study:

• To develop multiFLEX-LF, a computational tool for accurate quantification of protein modification extent in label-free proteomics.
• To enable precursor-centric analysis of entire datasets for identifying modification dynamics.

Main Methods:

• multiFLEX-LF builds on FLEXIQUANT, utilizing robust linear regression to determine modification extent relative to a reference.
• It analyzes label-free discovery proteomics data in a precursor-centric manner.
• Hierarchical clustering of precursors based on modification scores is used to study modification dynamics.

Main Results:

• multiFLEX-LF successfully applied to analyze anaphase-promoting complex/cyclosome (APC/C) modifications during mitosis using data-independent acquisition.
• Clustering identified varying modification dynamics and enabled ordering of modification events.
• The tool facilitates fast identification and quantification of differentially modified peptide precursors.

Conclusions:

• multiFLEX-LF provides a fast and efficient method for analyzing protein modification dynamics in large-scale proteomics studies.
• It supports time-series and case-control investigations of peptide precursor modifications.
• The tool is accessible for use on personal computers and available online.