FAQ: Do I need to deglycosylate my protein sample for proteomic analysis?

If a protein is glycosylated, any given fragment will be present as a collection of glycoforms since the same peptide that carry a variety of glycan structures. Proteomic analysis software is usually not designed to handle the myriad of possibilities that arise, therefore the fragments will remain unrecognized. This is the reason deglycosylation is often recommended prior to performing these experiments.