Proteomics/Mass Spectrometry

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Protocols

Gel staining
Many staining methods are compatible with subsequent tryptic digestion and mass spectrometric analysis. However, it is important that the proteins are not covalently modified or irreversibly fixed in the gel during staining. We prefer that you stain the gels by Coomassie blue stain (Bio-Safe) from Bio-Rad, Cat# 161-0786. If you choose to use silver staining, be careful to follow the suggested protocol below. Otherwise, it may not be possible to obtain any mass spectrometry data.

Coomassie Blue staining

1. Wash 3´ 5 min washes with ddH2O
2. Fix the gel with 40% methanol, 10% acetic acid, and 50% H2O for 60 min
3. Rinse the gel with ddH2O for 3 times
4. Wash with 50% ethanol, 50% H2O overnight to decrease the gel background at 4oC
5. Rinse with ddH2O 3 times
6. Stain the gel in Bio-SafeTM coomassie stain solution which is enough to cover the gel
7. Gently shake for 1 hour
8. Rinse with ddH2O for 3 times
9. Wash with ddH2O overnight
10. Wrap the gel with clean Sara wrap. Acquiring gel image can be done with a scanner. Never touch your gel with bare skin.
11. Store the gel in 1 to 2% acetic acid

Please contact us if you prefer to use other stain like SYPRO that is compatible with mass spectrometry.

Silver staining (Adapted from Blum et al, Electrophoresis, 8, pp93-99, 1987 and Schevchenko, A. et al. (1996) Anal. Chem. 68, 850-858)

1. Fix the gel in 50% ethanol, 5% acetic acid for 1hr.
2. Wash the gel in 50% ethanol overnight.
3. Wash gel in Milli Q H2O for 3´10 min
4. Sensitize gel in 0.02% Na2S2O3.5H2O for 1 min.
5. Wash gel in chilled H2O, 3´30 secs
6. Incubate gel in cold 0.1% AgNO3 for 20 mins. at 4 °C
7. Wash the gel in H2O 3´20 secs
8. Transfer the gel to a clean container
9. Wash the gel in H2O for 1 min.
10. Develop the gel in 0.05% Formalin, 3% Na2CO3 (To make 500ml of 0.05% formalin needs 0.25 ml of 37% formaldehyde)
11. Change the developing solution when the developer turns yellow.
12. Stop the staining with 5% acetic acid
13. Wash the gel 3´ 10 mins with ddH2O
14. Store the gel at 4 °C in 1% HAc

TCA Precipitation

1. Dilute protein to 500 ul with water in eppendorf tube
2. Add:
   • 50ul of DOC
   • 25 ul of TX 100
   • 80 ul of TCA (13%TCA)
3. At least 2 hrs on ice
4. Spin in a bench-top microfuge at 4 oC for 30 min at Max. speed (15,000 rpm).
5. There will be a flaky pellet up the side of the tube
6. Dump sup, let the tube stand on end on a kimwipe to get most of the liquid out. Don't sweat it if a little is left in the bottom
7. Add 500ul of ethanol/ether( cold aceton) . Bath sonicate to thoroughly disrupt pellet
8. On ice for 30 min
9. Repeat step 4
10. There will be little to no pellet
11. Repeat step 6
12. Let air dry at room temperature
13. Re-suspend samples in 5 ul running buffer first, then 20 ul sample buffer
14. Heat at 85 degree for 5 min.
15. Load sample to each well (25ul)

References

• Concentration and detergent removal
  
  • Sauve, D. M., D. T. Ho, et al. (1995). "Concentration of dilute protein for gel electrophoresis." Anal Biochem 226(2): 382-3.
  • Wessel, D. and U. I. Flugge (1984). "A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids." Anal Biochem 138(1): 141-3.
• Protein Precipitation by Trichloroacetic Acid
  
  • Brown, R. E., K. L. Jarvis, et al. (1989). "Protein measurement using bicinchoninic acid: elimination of interfering substances." Anal Biochem 180(1): 136-9.

Instrumentation | Fees Schedule | Sample Submission | Sample Preparation | Protocols | FAQ | Useful Links | Applications