Many proteoforms – arising from alternative splicing, post-translational modifications (PTM), 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 and derived an algorithm for optimal inference. We applied this algorithm to infer proteoform stoichiometries in two experimental systems that supported rigorous bench-marking: alkylated proteoforms spiked-in at known ratios and endogenous histone 3 PTM proteoforms quantified relative to internal heavy standards. When compared to the benchmarks, the proteoform stoichiometries interfered by HIquant without using external standards had relative error of 5 - 15% for simple proteoforms and 20 - 30% for complex proteoforms. A HIquant server is implemented at: https://web.northeastern.edu/slavov/2014_HIquant/
slavovLab@JohnRYatesIII@TheScientistLLC I agree, Academia gives the most family flexibility. Also, the things that I dislike about Academia seem to be a part of just about any other exciting and influential career option.
I am happy with my choices and not worried about myself.