I would like to learn about any computational tool for localization of glycopeptide after PNGase treatment?
Inamul,
if I understand you correctly what you want to know is where the glycan was located after you released it from a glycopeptide using PNGase F, correct? This is easy. The treatment with PNGase F releases the gylcan by hydrolysis and this converts the Asparagine in the NXS/T sequence into Aspartic acid. Thus the only thing you have to do is to tell the database search engine such as MASCOT that a deamidation on Asparagine is allowed. The search result will then usually show you the site of the deamidation based on MS/MS assignments. If you then observe deamidations in an NXS/T sequence, this was the former N-glcan attachment site. In case of doubt (e.g. several potential atachment site which is not very likely but still possible) you can look for score differences. For MASCOT, if the score difference between the best match and the second best match with the deamidation at a different position is bigger than 15-20 you can be pretty sure about the assignment. There is a paper on this by Bernhard Kuester from Munich on localization of phosphorylations by that way.
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