Rosalind: Learn bioinformatics by programming it (opens in new tab)

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.

The first paragraph of the expanded question text has: "every pair of adjacent amino acids has lost one molecule of water, meaning that a polypeptide containing n amino acids has had n−1 water molecules removed"

The second paragraph has: "Thus, the mass of a protein is the sum of masses of all its residues plus the mass of a single water molecule."

The fifth paragraph has: "The mass of a protein is the sum of the monoisotopic masses of its amino acid residues plus the mass of a single water molecule"

And the monoisotopic mass table says "Note: the monoisotopic mass of water is considered to be 18.01056 Da."

So I thought that the water molecule was important in the calculation.

However, the last paragraph (which I only now closely read) says it isn't important, with "In the following several problems on applications of mass spectrometry, we avoid the complication of having to distinguish between residues and non-residues by only considering peptides excised from the middle of the protein. This is a relatively safe assumption because in practice, peptide analysis is often performed in tandem mass spectrometry."

Since it didn't mention "water", and instead used the specialist term "residue", I missed the connection earlier.

That said, the text seems to use "residue" inconsistently. There's the definition "a residue is a molecule from which a water molecule has been removed; every amino acid in a protein are residues except the leftmost and the rightmost ones."

but there's also the usage: "the mass of a protein is the sum of masses of all its residues plus the mass of a single water molecule"

Surely that should be "the mass of a protein is the sum of masses of all its residues plus the mass of its leftmost and rightmost amino acids minus the mass of a single water molecule", yes?

So I looked up the definition of "amino acid residue". It appears to be https://goldbook.iupac.org/terms/view/A00279 "α-Amino-acid residues are therefore structures that lack a hydrogen atom of the amino group (–NH–CHR–COOH), or the hydroxyl moiety of the carboxyl group (NH2–CHR–CO–), or both (–NH–CHR–COO–); all units of a peptide chain are therefore amino-acid residues".

https://en.wikipedia.org/wiki/Protein_sequencing#Whole-mass_... also agrees that "residue" includes the two amino acids at the ends, saying "The protein’s whole mass is the sum of the masses of its amino-acid residues plus the mass of a water molecule and adjusted for any post-translational modifications"

Which means ... I don't think the author uses the term "residue" correctly?

Or, more likely, I'm confused by the specialist terminology. Can someone clear up my confusion?

> The monoisotopic mass is not used frequently in fields outside of mass spectrometry because other fields cannot distinguish molecules of different isotopic composition. For this reason, mostly the average molecular mass or even more commonly the molar mass is used. For most purposes such as weighing out bulk chemicals only the molar mass is relevant since what one is weighing is a statistical distribution of varying isotopic compositions.

> This concept is most helpful in mass spectrometry because individual molecules (or atoms, as in ICP-MS) are measured, and not their statistical average as a whole. Since mass spectrometry is often used for quantifying trace-level compounds, maximizing the sensitivity of the analysis is usually desired. By choosing to look for the most abundant isotopic version of a molecule, the analysis is likely to be most sensitive, which enables even smaller amounts of the target compounds to be quantified. Therefore, the concept is very useful to analysts looking for trace-level residues of organic molecules, such as pesticide residue in foods and agricultural products.