The present invention provides a method of determining the
absolute amount of a target polypeptide in a sample, said method comprising the following steps: (a) adding (aa) a fusion polypeptide to said sample, said fusion polypeptide comprising (i) at least one tag sequence and (ii) a subsequence of the target polypeptide; and (ab) a known
absolute amount of a tag polypeptide comprising or consisting of said tag sequence according to (aa) to said sample, wherein said fusion polypeptide on the one hand is
mass-altered as compared to said target polypeptide and said tag polypeptide on the other hand, for example, said fusion polypeptide on the one hand and said target polypeptide and said tag polypeptide on the other hand are differently
isotope labeled; (b) performing proteolytic
digestion of the mixture obtained in step (a); (c) subjecting the result of proteolytic
digestion of step (b), optionally after
chromatography, to
mass spectrometric analysis; and (d) determining the
absolute amount of said target polypeptide from (i) the peak intensities in the
mass spectrum acquired in step (c) of said fusion polypeptide, said tag polypeptide and said target polypeptide and (ii) said known absolute amount of said tag polypeptide.Furthermore provided is a fusion polypeptide for the quantification of a target polypeptide by mass
spectroscopy, wherein: said fusion polypeptide consists of 35 to 455
amino acid residues and comprises (i) a target region, which is a fragment of the target polypeptide, and (ii) a tag region, which is not a fragment of the target polypeptide, said target region consists of 15 to 205
amino acid residues and comprises at least two signature regions; said tag region consists of 20 to 250
amino acid residues and comprises at least two signature regions; and each signature region has the structure Y-Z-X4-28-Y-Z, wherein all Y:s are selected from one of (i)-(iv), wherein (i) is R or K, (ii) is Y, F, W or L, (iii) is E and (iv) is D and each X and each Z are independently any
amino acid residue, provided that the Z:s are not P if the Y:s are selected from (i)-(iii); and each signature region comprises at least one
amino acid residue comprising a
heavy isotope.