FLEXIQuant-LF

FLEXIQuant-LF quantifies the extent of protein post-translational modifications in label-free proteomics datasets to enable large-scale identification and relative quantification of differentially modified peptides without prior knowledge of modification type.

Key Features:

• Label-Free Quantification: Employs label-free quantification focused on unmodified peptides to establish baselines for assessing modification extent.
• Robust Linear Regression: Uses robust linear regression to estimate peptide modification extent and accommodate variability in proteomics measurements.
• Unbiased Identification: Identifies differentially modified peptides without requiring prior knowledge of the chemical nature of the modification.
• Scalability: Designed to operate on large-scale proteomics datasets to quantify modification extent across many peptides.

Scientific Applications:

• Understanding PTM Regulation: Quantifies modification extent to inform how post-translational modifications regulate protein function and cellular processes.
• Mitosis Studies (APC/C, DIA): Applied to data-independent-acquisition (DIA) datasets of the anaphase promoting complex/cyclosome (APC/C) to study dynamic protein regulation during mitosis.

Methodology:

Integrates label-free quantification focused on unmodified peptides with robust linear regression to quantify peptide modification extent, processes proteomics data without prior modification-type knowledge, and is applicable to LC-MS/MS and DIA datasets.