Lys-C OR Trypsin In-Solution Protein Digest Protocol
Original protocol from the J. Yates Lab, Scripps Research Institute
If you have not already done so, please read our sample preparation tips.
- Bring solution up to 8M Urea and 100mM Tris-HCl pH 8.5 (use 10 M urea and 1 M tris stocks; ideal final volume is about 80µl).
- Add 100 mM TCEP (a reducing agent) to a final concentration of 5 mM.. Incubate at room temp. for 20 min (2.5µl if the total volume was 80µl).
- Add 500mM iodoacetamide (make fresh daily) to a final concentratrion of 10 mM. Incubate at room temp. for 15 min. in the dark (covered with foil).
- Use one of the following enzymes (trypsin is recommeded for mudPIT):
- Dilute samples by a factor of four with 100mM Tris-HCl pH 8.5 (final urea conc. = 2M; if sample volume is a problem, dilute by only a factor of two to 4M urea)
- Add 100 mM CaCl2 to a final conc. of 1mM.
- Add in trypsin 1µl (0.5µg/µl) Promega sequencing grade trypsin is recommended.
- Incubate overnight at 37°C in the dark.
- Add in Lys-C 1µl (0.1µg/µl), 1/100th total amount.
- Incubate for 4 hr. at 37°C in the dark.
- Add formic acid to 5% final conc.
1ml MilliQ water
make a 1/10 dilution and store at –20°C in aliquots
500µl ddH2O, make fresh
ddH2O to 100ml
You may also access this protocol via a PDF for easier printing.