Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS)

By reporting the molar abundance of proteins, absolute quantification determines their stoichiometry in complexes, pathways, or networks. Typically, absolute quantification relies either on protein-specific isotopically labeled peptide standards or on a semiempirical calibration against the average abundance of peptides chosen from arbitrarily selected proteins. In contrast, a generic protein standard FUGIS (fully unlabeled generic internal standard) requires no isotopic labeling, chemical synthesis, or external calibration and is applicable to quantifying proteins of any organismal origin. The median intensity of the peptide peaks produced by the tryptic digestion of FUGIS is used as a single-point calibrant to determine the molar abundance of any codigested protein. Powered by FUGIS, median-based absolute quantification (MBAQ) outperformed other methods of untargeted proteome-wide absolute quantification.

Automated summary

Absolute quantification determines the stoichiometry of proteins in complexes, pathways, or networks by reporting their molar abundance. The use of a generic protein standard called FUGIS allows for quantification of proteins from any organism without the need for isotopic labeling or external calibration. Powered by FUGIS, median-based absolute quantification (MBAQ) outperforms other methods for untargeted proteome-wide quantification.