I was trying to analyze a compound who's MW is near to the MW of the matrix used in MALDI-TOF. So, will the matrix show any peaks if I run the sample on MALDI?
If the signal is intense, it should work using a matrix with the appropriate MW and solubility compatibility at the crystal level. It will largely depend on the physico-chemical properties of the analyte. If the signal is weak, use a high res instruments such as FTICR or Orbitrap. If the compound yields ions without matrix (LDI) is another option.
Matrix will definitely shows its own peaks. In fact people have been using matrix peaks as internal calibrants for a long time.
They key to your problem is to know the accurate mass of your matrix peak, so you can tell whether that peak comes from your sample or not. Of course you will also have the problem of ion suppression, but that depends on the chemical property and amount of your sample.
Yes the matrix peak should be visible, as has already been said. So you should check what can be going on if your matrix peak is not visible. You could be having problems of either chemical or instrumental nature. Another approach would be to explore the convenience and possibility of using a matrix-free methods, once they could eliminate some potential interference between your analyte and your matrix. Such methods are:
* SELDI
* Desorption ionization on silicon (DIOS) which is laser desorption/ionization of a sample deposited on a porous silicon surface. Nanostructure-initiator mass spectrometry (NIMS)
* Nanowire-assisted laser desorption/ionization (NALDI) which uses a target consisting of nanowires made from metal oxides or nitrides (Bruker)
* the same idea but using graphene as the substract.
As Vladimir says, you can explore alternative matrix-free methods, or you can also record the spectrum using different matrices. The only peak that such spectra should have in common is your analite`s peak.
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