This is completely based on our objectives. If it is aimed to study on the effect of fermentation on anti-nutritional factors, compare the level before and after fermentation. However, analyzing respective enzyme activity will be an advantages, since, most of the anti-nutrients were degraded by the microbial enzymes during fermentation.

The vast reports are available in the literature. For an example.,

The level of the phytic acid was significantly reduced post fermentation due to the activity of endogenous phytase enzyme produced by the microorganism, which are capable of hydrolyzing the phytic acid in the fermented food preparations into inositol and orthophosphate (Reddy and Peirson 1994). L. acidophilus, A. niger and S. cerevisiae had produced 198 U/mg, 58 U/g, and 0.7 U/mg of phytase, respectively during solid state fermentation as reported by Shivanna and Venkatesawaran (2015), Gull et al. (2013) and Ries and Macedo (2011). 

Tannin content was significantly reduced due to the production of enzyme tannase or microbial phenyl oxidase action during fermentation (Emambux and Taylor 2003). A. niger (Liu et al. 2016) and L. acidophilus (Sabu et al. 2006) has produced 12.26 and 0.85 U/g of tannase, respectively during solid state fermentation. However there are no available reports about tannase production using S. cerevisiae.

Makkar and Becker (1997) reported the production of glycosidase enzymes by microorganisms during fermentation which are likely to break saponin into sapogenin and sugar moieties. The reduction of glucosinolates mainly attributed to the utilization glucose and sulphur moieties during fermentation (Shi et al., 2015).

The following link may be useful for you

file:///C:/Users/TEMP.DESKTOP-LVKSUC2.011/Downloads/60341-180742-1-PB.pdf

Jannathulla R...........Thank you for your comprehensive explanation

It is not necessary. That depends of aim of fermentation.