The best thing you can do is expressions tests. You can grow 5ml cultures and test different induction time and conc of IPTG, different induction temperature. In the end you run and SDS PAGE and if your protein is over-expressing you should be able to see the most abundant protein corresponding to the expected molecular weight. If you don't see a clear over-expression band on the gel, your protein might be still expressing but probably not at high levels. 

Actually my problem is we have expressed 58KDa protein in pichia and after induction we are getting band on 48KDa  instead of 58KDa in SDS PAGE , ELISA and Western also its picking up. We observed there is no problems in SDS PAGE. What would be the reason.?

 Only MS can answer that, it could be a degradation problem or simply your protein has an extreme pI that affect the migration on the gel, it is common, so if you are able to purify it, you should sent it for MS.