I am enriching biotinylated proteins by Streptavidin pull-down, elution with 50mM Tris-Cl, 1%SDS, 1mMDTT, 25mM Biotin, followed by FASP of elution product and MS analysis. I get several hits, useful included. However, I can not detect any biotinylated peptides. Ideas, anyone?
Dear Neha,
You can check your biotinylation protocol. Are you sure that you have actually biotinylated the peptide? Sometimes the process can be sensitive to temperature, time, contaminants etc.
Secondly, if you have access to a biosensor like Attana, Fortébio, Biacore or similar you can always capture the biotinylated peptide on a strepavidin sensorchip and flow over an analyte that you know should interact with the peptide. If you use a crude samples for capturing the peptide I would recommend either the Attana or Fortébio instrument.
Good luck!
Teodor
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