Re bioinformatics /residues / lingo / life - bioinformatics is a catch all term for a set of loosely related tools being applied across the full field of disciplines. The early pioneers in bioinformatics (like Pevzner himself) were all physicists and electrical engineers who moved into the realm of biology. Your exact terminology is generally dependent on the specific problem you are solving and may be slightly different that the more general uses of the same words. Either way, I hope that if you are interested in the underlying topics that bioinformatics deals with, you won't let some issues in vernacular trip you up!
I tried to find some place which worked this out more than my earlier calculation. The closest was https://www.waters.com/webassets/cms/library/docs/720000807e... under the entry for "Molecular ion"
> The mass of the molecular ion corresponds to the nominal or monoisotopic mass of the molecule, with the mass of the electron added or lost usually consequential.
However, I can't help but think that last word should be "inconsequential."
I did find https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.8478#rc... which shows it's possible to measure the difference between ¹⁶O¹⁸O⁺⁺ and ¹⁷O⁺ ("The interference of ¹⁶O¹⁸O⁺⁺ can be detected 0.002 mass units before the larger ¹⁷O⁺ peak starts.") That must be due to binding energy as the naive charge/mass ratio is identical.
That's only 4x more than the 0.00054 mass units I estimated for an electron.
I looked at some of the other example problems. I do not think I am interested in this field.
Thank you for your exchange of information.
In high school I tried to build a mass spectrometer. It didn't work - I couldn't get a high enough vacuum, and a few years later as a physics undergrad did I find that that was only one of several problems I had. It was fun to try though.
But I do know that the ionized particle has a charge, and that electron affects the overall mass, by about 1/1836 Dalton . That's 0.00054 Dalton, while the table lists masses down to even higher accuracy, like 71.03711 .
The example output gives a value down to 3 decimal digits, so at that precision there's a 50% chance that the electron mass will affect the result.
Isn't this problem therefore implicitly teaching an excessive trust in significant digits?
Now, I suspect that the mass spectrometers they use aren't that accurate. But it's bugging me now.
As mbreese wrote elsewhere here, I'm (clearly) reading too much into the problem. I don't think bioinformatics is the right field for me.