In 65% of cases "purify by" is used
In practice you purify by slowly cooling a hot, saturated solution of your compound.
By the development of satipatthana the mind will be purified by right understanding.
As the priest and representative of the perfection or purifying by fire, and so he was called by its name.
May our Lord, when he cometh, pronounce us blessed, and present us to the Father, washed in his blood, purified by his Spirit, and fit to be partakers of the inheritance of the saints in light.
In 9% of cases "purify from" is used
It is said the Bayt al-Muqqadis is called so because in it the Holy Prophet (Sallahu? Alaihi Wasallam) was purified from wrong actions.
In 7% of cases "purify in" is used
The holy angel can also remind us of what still needs to be purified in our hearts.