Sample preparation (MS, LC-MS)

General recommendations for sample preparation for MS and LC-MS analyses.

Samples

All samples must be soluble in the mobile phase used in the (LC-)MS system. If insoluble sample is injected, it will precipitate-out and get the system stuck.

Solvents

In all cases, use solvents compatible with the mobile phase used in the (LC-)-MS system. That means:

  • For ISQ in Wing4, use either methanol, or water-methanol mixtures. If you are using water as a mobile phase, dissolve your sample in water.

  • For ISQ in Mercator and LCQ-Fleet, use well-diluted water-acetonitrile mixtures or methanol. Samples rich in acetonitrile or methanol can cause bad separation and clogging of the instrument in some cases.

Concentration recommendation

Generally, it is good to start with a 10μM solution of your sample. The optimal sample concentration depends on a sample ability to form ions (ionizability). Please refer to your MS tutor for concentration recommendations in your specific case.

For the LC-MS system located in wing 1 (ISQ mass spectrometer - Mercator (LC-MS)) you can use slightly higher starting concentrations around 50μM at your own risk. This difference is because the sample gets a bit diluted on the column.

Good sample concentration is a concentration at which you see your analyte and at which the sample is not polluting the system at the same time. Avoid too concentrated samples both for ISQ and for Accurate Mass sample submission.

Pollutants

Small capillaries and valves are used both in LC and in MS. Any small particles could stuck those parts and thus leads to instrument down-times. In addition, some compound notoriously negatively impairs mass spectra and causes suppression of your desired ion signal.

List of known pollutants

  • polar aprotic solvents (DMF, HMPA..)

  • buffers (TEAB ..) and concentrated ionic/easily ionizable compounds (TEA, DIPEA..)

  • electrolytes (TBAF, TBAPF6, …)

  • molecular sieves, microcrystalline compounds

  • low-grade solvents

  • concentrated samples

  • plastics, plasticizers

  • triphenylphosphine-oxide

Gray-zone compounds

These compounds lead to ion-suppression and thus to signal impairment. However, they can be washed-out relatively easily when they are used in low concentrations. Their use is discouraged, but still allowed for special cases. Take special care to check that the instrument is free of those compounds once you’re finished.

  • DMSO:

    Although it belongs to polar aprotic solvents, it can be washed-out relatively easily. Use it in low concentrations[1] and always afterwards wash the system by blank runs up to the point where the signal of DMSO is absent (dimethyl sulfoxide, m/z 157 - 2x DMSO+H+, m/z 169 - 2x DMSO-d6+H+).

  • TFA (trifluoroacetic acid):

    Commonly used as an additive for liquid chromatography (0.025-0.1%). It tends to form ion-pairs with cations in the gas phase.[2] Can be partly countered by additives.[3] It can be washed out easily.

Methods for preparing a sample

Methods for preparing samples differ from group to group. Please refer to your MS tutor for sample preparation method in your specific case.

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