Hello Navin,
Just to clarify, have you defined the field as part of the SKUInfo object, in:
Development -> Modules -> E-commerce -> Classes -> SKU
The where condition is executed directly on the SQL server, so as long as the Field name matches, it should filter the returned data. Are you seeing any SQL exceptions in the Event log that would suggest the field name is incorrect?
Could you please post the code where you build the where condition?