MALDI-TOF is suitable to identify whether a protein is a dimer or a trimer?

Achim Recktenwald, PhD achim at
Mon Jan 27 08:15:38 EST 1997

Leemor Joshua-Tor wrote:
> >MALDI-TOF analysis is suitable to identifying whether a protein is a
> >homodimer or a homotrimer?
> >
> >I have a small DNA-binding protein(6,100 dalton) quite well purified.
> >Through size exclusion HPLC gel chromatography, I found its effective
> >molecular weight of the protein in the absence of its binding DNA
> >sequence is about 19,000 dalton, close to homotrimer.
> >But I am not sure that it is a trimer based on only the result becuase I
> >didn't ever hear about homotrimer DNA binding protein; so I need some
> >additional experiments confirming this fact.
> >
> >Thank you for your time and expertise,
> >
> >Lee, Ji Hyun
> The best, most accurate, way to determine the molecular weight of your
> sample and thus it's oligomeric form is by analytical ultracentrifugation.
> Another example of a trimeric DNA-binding protein is the heat shock
> transcription factor.

The accuracy of MALDI-mass-spectrometers is in the range of 0.1%; 0.1%
of 6100Da is 6.1Da; 0.1% of 19000Da/2 is 9.5Da. So in both cases you are
well in the specifications. 
If you want the mass very exact, look for a lab with an electrospray
mass-spectrometer. In the range below 10kDa the accuracyy is probable
better than 1Da.


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