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To detect the deamidation from Glutamine to Glutamate in a protein, normal practise seems to be a mass spec, where it is claimed there is a change of 1 dalton.

EG It is claimed that:

Deamidation of an Asn to Asp/IsoAsp results in an increase in mass of a single dalton.

But when I look at their table, they are using Glutamic Acid as being 1 Dalton heavier than Glutamate, but at pH 7 the Glutamic Acid will be deprotonated to Glutamate. Do they put the sample in pH 4 to protonate the Glutamate first? But then you are risking catalysing the hydrolysis of Glutamine anyway, rendering your results useless!

There should be a charge difference though, as you are going from neutral to a negative charge, so that would show up in a change in mass/charge on the mass spec, rather than a mass change.

Any help would be appreciated.

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This might be better on chemistry SE. –  dd3 Jul 22 '13 at 21:07
    
Its more relevant to Biology as its to do with Proteins I think. –  Nick Jul 22 '13 at 21:30
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I am not an expert in this area but this is what I understand. Usually ESI based protein mass spec imparts a positive charge on the proteins by protonation. Formic acid is usually added to help in protonation. In deamidation -NH2 is replaced by -OH thereby increasing the mass by 1 dalton (14+2 -> 16+1). I think that glutamine may be also acquire multiple charge (by NH2 protonation). You can see this article, which talks about dealing with deamidation artifacts resulting from sample preparation techniques. –  WYSIWYG Jul 22 '13 at 21:46
    
Ah, so the samples are put in acidic conditions to protonate the glutamate which can result in false positives, interesting. –  Nick Jul 23 '13 at 7:10
    
Biochemistry is still chemistry :) –  MattDMo Jul 23 '13 at 16:04
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