Hi,

You could consider having stable isotope-labeled variants made of the so-called 'proteotypic' peptides of all your proteins of interest.

You can look up the details on the net, but what it comes down to is that proteotypic peptides are unique to a single protein and are not prone to any form of post-translational modification, such as methionine oxidation or asparagine deamidation (i.e. devoid of these amino acids). And they should have reasonable length, to ensure proper retention on column as well as ionization (and fragmentation) properties in the MS.

It can be costly, but provides an elegant way to internally standardize your assay, especially if you have them made in one sequence and that the proteotypic peptides are released only during the proteolytic digestion in your sample preparation.

Hope this helps!

Somayesadat Heidary Be careful to design amino acid sequences of peptides when you measure enzymatic (tryptic) digests as samples for LC-MS/MS.

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