If a dust peak happens to fall right on top of a peak of interest, should that spot be included in the analysis even though the dust particle will skew the results for that peak?
Dust particles effect the accuracy of quantitation and the Student’s T-test result but you may wish to include the spot in the analysis since it occurs on a protein spot that is of interest. Therefore you should include it and add a comment in the spot comment field such as ‘includes dust’. If you have replicate gels this result can then be checked to see if it is a consistent difference in the other gels, either by matching in BVA or manually having a look at the other gels in DIA. In DeCyder Differential Analysis Software, quantitation is based upon spot volume. The volume of a dust particle is very small in comparison to the majority of spots and therefore dust should not impact too greatly on the analysis of that particular spot. However, it should be remembered that low abundance proteins, with smaller spot volumes, will be affected to a greater extent. Subsequently if the dust particles skews the accuracy of quantitation by a large amount it should ultimately be excluded from the
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