We recommend adhering to the method as stated as this is how the kit has been validated, any deviation from this method will need to be internally validated.
However, if it is necessary to alter the procedure we would suggest running the control as the samples are run.
If the correct value for the control is obtained, it is possible to conclude the method deviation did not have any effect on the assay results.
There are essential steps to this procedure which we do not recommend changing such as the incubation in the linear shaking water bath. The linear shaking step during this method is extremely important (see paper attached). We recommend if this is altered and if it is possible, to somewhat mimic this motion with alternative equipment it is possible to use it for comparative purposes.