Disclosed is a method of characterising two samples of an unlabelled protein, the method comprising: (i) providing a sample of a labelled protein, having a known amino acid sequence, wherein at least one amino acid in the protein is replaced with an isotopically labelled amino acid (ii) providing a first sample comprising the protein, wherein the protein is not isotopically labelled (iii) mixing the labelled protein and the unlabelled protein from the first sample to form a mixture (iv) subjecting the mixture to protein digestion to form a first digest (v) subjecting the first digest to bottom-up Liquid Chromatography-Mass Spectroscopy to form a first spectra including intensities of individual mass-to-charge (m/z) peaks corresponding to individual peptide fragments of the labelled protein and the unlabelled protein from the first sample (vi) summing the intensities of the m/z peaks associated with a peptide fragment of the labelled protein (vii) summing the intensities of the m/z peaks for the corresponding peptide fragment of the unlabelled protein from the first sample (viii) calculating the ratio of the sum of the m/z peaks for the peptide fragment of the unlabelled protein from the first sample over the sum of the m/z peaks for the peptide fragment of the labelled protein (ix) providing a second sample comprising the protein, wherein the protein is not isotopically labelled (x) mixing the labelled protein and the unlabelled protein from the second sample to form a mixture (xi) subjecting the mixture to protein digestion to form a second digest (xii) subjecting the second digest to bottom-up Liquid Chromatography-Mass Spectroscopy to form a second spectra including intensities of individual mass-to-charge (m/z) peaks corresponding to individual peptide fragments of the labelled protein and the unlabelled protein from the second sample (xiii) summing the intensities of the m/z peaks associated with the peptide fragment of the labelled protein corresponding to the
