Perhaps.  Depends where the clipping is taking place.  Many enzymes are activated by clipping.  Most labs use 'ion exchange' chromatography.

How much are you "clipping"? There are numerous examples in the literature of proteins in their glycosylated forms from the free polypeptide. See, for example, the resolution of the glycoprotein, Ribonuclease B from its non-glycosylated version, Ribonuclease A. It is possible to get resolution of the different glycosylated forms (e.g., those missing one or more mannose units compared to the complete Ribonuclease B. Besides ion exchange chromatography, you can also use hydrophobic interaction liquid chromatography (HILIC) (see attached). You can also find very high resolution of glycoforms with some of the "ion chromatography" (as opposed to ion exchange chromatography) in the online examples from the Dionex section of the Thermo Fisher website (look up Pro-Pac). Some people have obtained good results for some glycoproteins with simple reversed-phase HPLC although that is not too common. Also, since some proteins are very heavily glycosylated you can sometimes see resolution with size exclusion separation. Since some glycoproteins are decorated with acidic carbohydrates, they are affected more by ion exchange than those that merely have a mass change.