Input normalization and PTM stoichiometry in Spectronaut

Post-translational modifications (PTM) 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 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 PTM site quantity.

In this poster, we present the novel support for input normalization and PTM site occupancy in Spectronaut^® version 19 for label-free DIA data, in addition to the existing PTM localization support. By using existing publicly available ground truth data, we validate the implementation of input normalization, as well as stoichiometry calculations based on flyability ratios.