Protocols

Below you will find several general procedures than have proven compatible with mass spectrometry. Please note that samples vary dramatically and the conditions (i.e., methods, concentrations, reagents, etc.) must be optimized for each sample type.

When considering using mass spectrometric analysis for the first time or when starting a new project, please call the Facility (618-453-6428) with questions/concerns regarding analysis of your samples.

Sample Preparation for MS (Must Read!)

Below you will find a number of guidelines that should be followed when preparing a sample for mass spectrometric analysis.

All samples should be submitted in polypropylene microcentrifuge tubes/vials (for peptides or proteins samples) or deactivated glass vials with Teflon-lined screw caps (for small molecule samples). Use a small volume insert if a limited amount of sample is available.
All sample tubes must be labeled with a sample ID and be accompanied by a sample submission form.
For MALDI analysis, please submit at least 1mg of purified solid sample or 50uL of (at least) 10pmol/mL sample solution prepared in compatible solvent(s) or a volatile buffer.
For electrospray analysis, please submit 50uL of (at least) 10pmol/mL sample solution prepared in 50% acetonitrile.
Solvents that are compatible with MALDI include acetonitrile, methanol, isopropanol, ethanol and water.
A volatile buffer such as ammonium acetate should be used whenever pH control is necessary. The maximum concentration that can be tolerated is 50 mM.
Allowable detergents include n-octyl-glucoside, n-dodecyl-glucoside, octanoyl-N-methylglucamide and decanoyl-n-methylglucamide
Avoid using:
- Tris, phosphates, citrates, and HEPES
- Urea and guanidinium salts
- TFA (acts as strong ion-pairing agent in electrospray)
- Detergents such as SDS, CHAPS, PEG, Tween, and Triton
- DMSO, acetates and glycerol
The presence of any of the above chemicals can completely suppress ionization of the sample making the difference between a successful or failed analysis.

Protein Staining (Compatible with MS) Coomassie Staining Silver Staining

In-Solution Tryptic Digestion

In-Gel Tryptic Digestion

Coomassie Stained (1D) Coomassie Stained (2D) Silver Stained (1D) Silver Stained (2D)

Reverse Phase C₁₈ Cleanup and Concentration for Peptides

Comments: Mary Kinsel