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0 pointseesmith6y ago0 comments

You wrote: "The value of monoisotopic values decreases as the size and complexity of the molecule goes up."

Yes, that is is agreement with the text I quoted earlier - "it became common practice to characterize molecules in the mass range of up to approximately 10 kDa by their monoisotopic masses".

Note (from another part of the second link I gave) "This eight amino acid peptide was named GmPep914 (DHPRGGNY), based on its monoisotopic mass."

So, there's plenty of clear evidence that people do use monoisotopic masses for mass spectra analysis of at least some peptides.

What is your point? That this question is poorly written? I think I started this thread to point that out.

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3 comments · 1 top-level

DrScientist6y ago· 2 in thread

My point was that while for small molecules, the mono-isotopic mass makes perfect sense as it's the major species, for larger proteins it isn't and indeed becomes a vanishingly small proportion.

Note for something around 10kda the difference between the average and mono-isotopic mass will be around ~6 daltons - with the experimental accuracy around ~1 dalton!

eesmithOP6y ago

You write now that it makes perfect sense.

However, at https://news.ycombinator.com/item?id=22383816 you wrote "even if broken down to small peptides in the mass spec, ... then monoisotopic makes no sense".

It was that latter point that I contested, because the literature clearly indicates that for at least some small peptides it makes sense.

DrScientist6y ago

Depends on your definition of small - but I accept the point that if the peptides are small enough it can be useful and I went too far there.

Remember the problem posed was to calculate the mass of proteins upto 1000aa where the difference between mono-isotopic mass and real average mass would be many 10's of daltons - much more than the missing water!

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