Optimization of a Label-Free Peptide Quantitation Strategy for Analysis of Therapeutic Proteins

Insights from Roche’s Assessment and Byos Implementation

The accurate quantitation of post-translational modifications (PTMs) in therapeutic proteins presents a significant challenge in mass spectrometry (MS) analysis due to factors like multiple charge states, missed cleavages, and low signal intensities of modified species. The effectiveness of quantitation strategies varies, with some methodologies focusing on the most intense charge state of a single species, potentially overlooking important variables like missed cleavages. Label-free quantitation offers relative measurements suited only for trend analysis, yet consistency in quantitation strategy is vital throughout drug development to evaluate the risks associated with PTMs. Roche’s work, supported by Protein Metrics software, underscores the importance of selecting an accurate strategy for PTM analysis, demonstrating the application of a customized report template and dynamic columns feature to optimize label-free peptide quantitation strategies, thereby addressing the challenges in ensuring the efficacy of therapeutic proteins.

This session was recorded in February 2024.

Key Learning Objectives

  • Six quantitation strategies compared for label-free peptide quantitation.
  • Preferred strategies implemented in Byos® for PTM and variant analysis.
  • Byos reports feature customizable dynamic columns for data analysis.