I am working on enrichment of glycopeptides using hilic materials. I dont have facility of LC/MS to detect the glycopeptides. What other way is best to identify glycopeptides from a MS spectrum? I have used GlycoMod to identify peptides but many glycopeptides which GlycoMod does not confirm while literature confirms.
How to identify glycopeptides?
Hi,
So you're trying to see if any peptides you've enriched are glycosylated, but unable to use mass spec for that?
What means do you have to analyse your peptide fractions? You could consider enzymatically deglycosylating your enriched peptides and see if their behavior, e.g. on LC, changes.
Identifying glycopeptides without access to LC-MS can indeed be challenging
You can try the following strategies
#Enzymatic Digestion and Peptide Mapping:
- Use enzymes like trypsin to digest your glycoprotein sample. Perform peptide mapping using techniques like SDS-PAGE or HPLC. While this won't directly identify glycopeptides, it can provide information about the peptide backbone.
#Periodate Oxidation:
- Periodate oxidation followed by chemical derivatization can be used to selectively cleave glycosidic linkages in glycopeptides. Analyze the resulting fragments to gain insights into glycosylation.
#Lectin Blotting:
- Employ lectin blotting techniques where lectins specific to certain glycan structures are used to detect glycopeptides. This can give an indication of glycosylation patterns.
#Immunoprecipitation:
- Use antibodies specific to glycopeptides or glycoproteins for immunoprecipitation. This can enrich the glycopeptides from your sample, and subsequent analysis can provide insights.
#Matrix-Assisted Laser Desorption/Ionization (MALDI):
- While not as high-resolution as LC-MS, MALDI-TOF mass spectrometry can be used for direct analysis of glycoproteins. It might not provide detailed structural information but can confirm the presence of glycosylation.
7. **Literature Mining:**
- Explore existing literature for similar glycoproteins or glycopeptides. Compare your findings with known glycosylation patterns and structures reported in the literature.
While these approaches may not offer the same level of detail as LC-MS.
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