  This letter is a response to the comments of Serang (2012) on Huang and He
(2012) in Bioinformatics. Serang (2012) claimed that the parameters for the
Fido algorithm should be specified using the grid search method in Serang et
al. (2010) so as to generate a deserved accuracy in performance comparison. It
seems that it is an argument on parameter tuning. However, it is indeed the
issue of how to conduct an unbiased performance evaluation for comparing
different protein inference algorithms. In this letter, we would explain why we
don't use the grid search for parameter selection in Huang and He (2012) and
show that this procedure may result in an over-estimated performance that is
unfair to competing algorithms. In fact, this issue has also been pointed out
by Li and Radivojac (2012).
