Sample Preparation

The following guidelines will be helpful and should be followed when you prepare samples for mass spectrometric analysis.



  • In general, volatile, low MW protic solvents are preferred, such as acetonitrile, methanol, isopropanol, ethanol, and water. In the LC-ESI-MS analysis, methanol/water (1:1) is the default solvent.
  • If water is required for solubility, up to 50% water may be added.
  •  Avoid using:
    * Tris, phosphates, citrates and HEPES
    * Urea and guanidinium salts
    * Trifluoroacetic acid (TFA) causes signal suppression and should be kept below 0.1%. Commonly used alternatives to high concentrations of TFA are mixtures of either 1% acetic or 0.1% formic acid with 0.025% TFA.
    * Detergents such as SDS, CHAPS, PEG, Tween, and Triton
    * DMSO, DMF, THF, acetates, and glycerol
    * Hydrocarbon solvents, such as hexane and benzene, are not amenable to ESI

Concentration and Volume

A reasonable sample concentration is critical to successful analysis, and extremely low or extremely high concentrations have detrimental effects. For electrospray analysis, please submit 50 ul of (at least) 10 pmol/ul sample solution. For MALDI analysis, please submit at least 1 mg of the purified solid sample or 50 ul of (at least) 10 pmol/ul sample solution. The samples should be submitted in polypropylene microcentrifuge tubes/vials or deactivated glass vials with Teflon-lined screw caps. Use a small volume insert if a limited amount of sample is available. All sample tubes/vials must be labeled with a sample ID and be accompanied by a Sample Submission Form (PDF or MS-Word).


How to Choose an Appropriate Ionization Method for Your Compounds

Please refer to the following descriptions of the ion sources:








Ionization Mechanism

Ionization Method Comparison


Please contact the facility if you have any questions or concerns regarding the preparation and analysis of your samples.