  Many proteoforms - arising from alternative splicing, post-translational
modifications (PTMs), or paralogous genes - have distinct biological functions,
such as histone PTM proteoforms. However, their quantification by existing
bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific
biases. To avoid these biases, we developed and implemented a first-principles
model (HIquant) for quantifying proteoform stoichiometries. We characterized
when MS data allow inferring proteoform stoichiometries by HIquant, derived an
algorithm for optimal inference, and demonstrated experimentally high accuracy
in quantifying fractional PTM occupancy without using external standards, even
in the challenging case of the histone modification code.
  HIquant server is implemented at:
https://web.northeastern.edu/slavov/2014_HIquant/
