FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data.

Area of Science:

• Proteomics
• Biochemistry
• Computational Biology

Background:

• LC-MS/MS advancements allow identification of thousands of modified peptides.
• Quantifying the extent of post-translational modifications (PTMs) is crucial for understanding protein regulation.
• Existing methods often require prior knowledge of specific PTM types.

Purpose of the Study:

• Introduce FLEXIQUANT-LF, a novel software tool for large-scale identification and quantification of differentially modified peptides.
• Enable quantification of PTM extent without prior knowledge of modification types.
• Provide a method for unbiased assessment of PTMs in quantitative proteomics.

Main Methods:

• Developed FLEXIQUANT-LF utilizing label-free quantification of unmodified peptides.
• Employed robust linear regression to accurately quantify peptide modification extent.
• Applied the software to data-independent acquisition (DIA) proteomics data.

Main Results:

• Demonstrated successful large-scale identification of differentially modified peptides.
• Quantified the modification extent of peptides in APC/C complex during mitosis.
• Validated the software's capability for unbiased PTM analysis.

Conclusions:

• FLEXIQUANT-LF offers a powerful approach for analyzing PTMs in large-scale proteomics studies.
• The tool enhances understanding of PTM function and regulation by quantifying modification extent.
• Software availability facilitates broader application in biological research.