A Comprehensive Solution for PTM Analysis: Integrating Input Normalization and Improved Stoichiometry Calculations

Post-translational modifications (PTMs) can dramatically alter the function of proteins and have important roles in disease and health as biomarkers or pharmaceutical targets. An important aspect of PTMs is the relative rate of site occupancy or PTM stoichiometry, which can provide biological information irrespective of the underlying protein abundance.

In proteomics experiments where modifications are studied using an enrichment step, it is important to decouple the changes in PTM site quantity from the changes in protein abundance in the original sample. This is achieved by performing input (pre-enrichment samples) normalization of the PTM site quantity.

In this poster, we present the support for input normalization as well as improved PTM stoichiometry calculations in Spectronaut 20 for label-free DIA data. By using existing publicly available ground truth data, we validate the implementation of input normalization, as well as stoichiometry calculations based on an improved 2-points flyability ratio algorithm.