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:
   • Peptide labeling: In this approach the peptides can be either isotopically labeled during cell growth (SILAC, N15 & O18) or post protease digest labeled (iTRAQ,TMT) to differentiate the samples for the quantification purpose.
   • Label free quantification: We are now offering label free quantification using Maxquant LFQ algorithum.
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.