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Protein Quantification in Complex Protein Mixtures

For mass spectrometry base protein quantification of a given proteome, the proteome is digested using a protease and subsequently the resulting peptides are analyzed and quantified using a mass spectrometer. There are two major approaches to protein quantification:

  1. Relative quantification of a protein from one sample to another:
  2. Absolute quantification of a protein or proteins in a sample: In the AQUA approach proteolytic peptides of a protein are first identified and characterized. From the characterized peptides a few sequences are selected and chemically synthesized using isotopically labeled amino acids, to differentiate these peptides from their native forms, and are spiked into the proteolytic digest to be used as internal standards for the peptide quantification.