Removal of Endo F2 by Magnetic Beads (P0772)

Materials:
Endo F2 (NEB #P0772)
Chitin Magnetic Beads (NEB #E8036)
Magnetic Separation Rack (NEB #S1506, NEB #S1509)

1. Pipette 50 µl Chitin Magnetic Beads (NEB #E8036) into an eppendorf tube and place the eppendorf in a magnetic separation rack (NEB #S1506 or #S1509). Let the magnet attract the chitin beads, then pipette off the liquid supernatant and discard.
2. With the eppendorf on the magnetic separation rack, wash the magnetic chitin beads 3 x 500 µl with
   50 mM NH₄ Formate pH 4.4 (or buffer of choice). Pipette of the supernatant and discard.  
3. Add the deglycosylated glycoprotein sample into the eppendorf with magnetic chitin beads.
4. Rock the deglycosylated glycoprotein sample with the magnetic chitin beads for 10 minutes at 4°C.
5. Place the eppendorf back on the magnetic separation rack, and allow the magnet to attract the chitin beads. Pipette off the supernatant and keep.  
6. Wash the magnetic chitin beads 3 x 100 µl with 50 mM NH₄ Formate pH 4.4 (or buffer of choice).
   Pipette of the supernatant from each wash and keep.  
7. Combine all supernatants from Steps 5 & 6, as these are the deglycosylated glycoprotein.
8. Analyze sample by method of choice.

Notes on Use:

1. Removal of Endo F2 from the deglycosylation reaction can be scaled up or down linearly with larger or smaller magnetic chitin bead volumes.
2. The chitin magnetic beads binding capacity is 0.4 µg/µl of CBD-tagged protein. The concentration of
   Endo F2 Lot 1 is 0.28 µg/µl.