So the enzyme activity is calculated as either increase of product concentration [P] or decrease in substrate concentration [S].

In practise, it's determined often using e.g. spectrophotometer as a single value, either change of absorbance of substrate/product or consumption of cofactor etc.

But if you use e.g. HPLC for determination of the amount of product and substrate in the reaction mixture, you can either simply use the amount of product formed ( [P] ) or how much product is in total of substrate and product ( [P]/[S]+[P] ).

Like in the beginning, I was measuring cis-trans isomerisation. To avoid mistakes due to bad pipetting etc. I always calculated how much % the trans isomer is from the pool.

Now I performed some purification and got some inconsisent data, as in two samples the total amount of my substrate+product was decreased. Thus I don't know which way I should go?

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