what exactly does this involve ..?
That depends!
First of all, are you working in a highly regulated area (e.g., pharmaceutical, clinical, environmental, etc)? if you are not, then any requirement for "certification" would be defined by government regulations (Canada is different from the US and Quebec is different from Ontario).
If you are working in a regulated area, then are you subject to GLP (Good Laboratory Practice) or GMP (Good Manufacturing Practice) regulations? If you don't know, find someone in your company who works in "regulatory affairs" whether your lab is subject to those regulations (things like QC will certainly be subject to GMP; development labs, formulations, pharmacokinetics probably GLP; early-stage discovery may not be covered by either).
If you fall under the "GxP" umbrella, then you should have SOPs (Standard Operating Procedures) in place that define how and how frequently you do instrument Qualification. Your instrument manufacturer should be able to provide you with draft procedures for PQ (Performance Qualification) of your systems, but you will probably have to adapt them to fit the specifics of the kinds of things you are doing. Commonly, SOPs will require that PQ be carried out any time an instrument is returned to use after service in order to verify that it is operating properly, and PM (Preventive Maintenance) be done on a regular (often annual) basis.