I have relative abundance data from a label free mass spectrometry experiment of a simple mixture of proteins (for simplicity call them protein A and protein B). These two proteins are similar in size, and I know the amount of protein A that was spiked into the mixture. If the relative abundance of protein A is 25% and protein B is 75%, can I estimate the total mass of protein B by the equation Mass_B = (Mass_A / MolecularWt_A) * 3 (conversion factor from relative abundance data) * MolecularWt_B?
No. You can never assume that different compounds will ionize in the same manner. MS analysis is not a "universal" detection technique.
Hi Tony,
I totally agree to William's answer.
However there is one possibility to overcome this problem by using the "Top 3" quantification approach (publication attached) just in case you are doing a bottom up analysis by using peptides of your protein samples.
Best,
Murat
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