Tips for Sample Preparation

Sample quantity
The resolution and sensitivity of Autoflex MALDI and Micromass Q-Tof 2 are superior. It appears that samples at 200 fetomoles may be enough for a protein ID. However, to achieve high accuracy, we would like to have sample at 1 -2 pmoles (100 ng of 100 kDa protein=1 pmol). For the SDS-gel sample, if a band is visible with Coomassie blue stain (detection limit, 100 ng), there is probably enough material present for protein ID.

Solvent
Using the appropriate solvents is very important for mass spectrometry. Volatile solvents such as methanol and acetonitrile are good for mass spectrometry. Avoid using DMSO, DMF, and large polar solvent. Always use spectroscopic grade solvent to prepare the sample.

Mixture and Impurities
Pure samples always provide more satisfactory data. Multiple component samples will compete for protons in the ionization process. The components with the highest concentration will give strongest signal; and the components with low concentration will give weak signals. In this case, the weak signals (desired peaks) will be suppressed. However, this can be circumvented when liquid chromatography is configured with the electrospray mass spectrometry to separate components.

Salts and Buffers
Salts and buffers are, in general, detrimental to MS analysis. Salts normally form adduct peaks which compete with the molecular ion peaks and broaden the overall signal (especially for protein analysis). ESI-MS is sensitive to salts and buffers resulting in signal suppression. Less than 1mM salts and buffers is recommended although higher salt concentrations may be tolerated. Ammonium acetate usually do not affect the signal greatly below 20 mM. However, sodium and potassium can be a real problem above 10mM.

Protein/Peptide sample handling