O-glycan preparation for MS analysis (all sample types)


To isolate O-glycan for mass spectrometry analysis.


Glassware and glass tubes are cleaned with Milli Q water and dried beforehand.
Reagents are weighted on aluminum foils with utensils clean with Milli Q water beforehand. Whenever possible, liquid reagents are handled with disposable glass pipettes.
Solvents are HPLC grade or higher.

The starting material in most cases is N-glycan-free (with PNGaseF or other methods) glycopeptides.


  1. Prepare a 0.1 M NaOH solution. This can be quickly made in a 50ml falcon tube by mixing 20 ml of MilliQ with one pellet of NaOH (Sigma-Aldrich, #S8045).
  2. Add 1 ml of 0.1 M NaOH to 55 mg of NaBH4 (sodium borohydride, Sigma-Aldrich, #213462) in a clean glass tube, mix well.
  3. Add 400 µl of the borohydride solution to a lyophilized sample in a screw-capped glass tube and close the tube.
  4. Incubate at 45°C overnight (14-16 hours).
  5. Terminate the reaction by adding 4-6 drops of pure (100%) acetic acid (Fisher, #A414-1) or until fizzing stops.
  6. Prepare the Dowex ion exchange resin. A stock solution of Dowex 50W X8 (mesh size 200-400) (Sigma-Aldrich, #44519) is made by washing three times 100 g of resin with 100 ml of 4 M HCl (hydrochloric acid, Fisher A144SI-212). Wash the resin with 300 ml of MilliQ water and repeat this wash step ~15 times until the pH remains stable. Then wash the resin with 200 ml of 5% acetic acid three times. This stock solution is table for up to one year stored at 4°C.
  7. Assemble a desalting column with 2-3 ml of the Dowex resin prepared above in a small glass column (such as a glass Pasteur pipette). Wash the column with 10 ml of 5% acetic acid.
  8. Load the acetic acid-neutralized sample onto the column and wash with 3 ml of 5% acetic acid. Collect and pool flow through and wash.
  9. Lyophilize the collected material.
  10. Add 1 ml of acetic acid: methanol (Fisher, #A452-4) solution (1:9; v/v=10%) to the lyophilized sample. Vortex thoroughly and dry under a stream of nitrogen. Repeat this co-evaporation step three more times.
  11. Condition a C18 Spe-Pak column (column size depends on the sample) with methanol, 5% acetic acid, 1-propanol (Fisher, #A414-1) and 5% acetic acid.
  12. Resuspend the dried sample in 200 µl of 50% methanol and load onto the conditioned C18 column. Wash the column with 4 ml of 5% acetic acid. Collect and pool flow through and wash.
  13. Lyophilize the sample and proceed to permethylation.