Comment by ihunter2839 | Hacker News Reader

Comment by ihunter2839 | Hacker News Reader

Parent Full thread

IANAP (really, IA(BARELY)AB), but I am not exactly clear where these additional electrons are sneaking in. Either way, I'm not sure the change would be significant enough to move the spectral peak outside of the range for a specific residue. There are lots of false peaks, and a lot of pre / post processing goes into managing those complexities.

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!

https://en.wikipedia.org/wiki/Dalton_(unit)#Measurement says "Although relative atomic masses are defined for neutral atoms, they are measured (by mass spectrometry) for ions: hence, the measured values must be corrected for the mass of the electrons that were removed to form the ions, and also for the mass equivalent of the electron binding energy,"

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.

Reply on news.ycombinator.com