Reading an MS report that only gives you a single number

Desalting before analysis: some samples need desalting to remove salts that suppress the peptide signal. Report whether desalting was used, because it can affect the apparent ionization efficiency and the reported purity.

I have said this before in a thread nobody could find, so it is worth repeating.

Where I part company with post #33, and it is a narrow parting.

Positional isomers and epimers are mass-identical. Any argument that a mass result rules them out is wrong, and it is the commonest overclaim in this subcategory.

Positional isomers and epimers are mass-identical. Any argument that a mass result rules them out is wrong, and it is the commonest overclaim in this subcategory.

The rule of thumb is fine; the edge cases are where it earns its keep.

Narrowing post #68, because the general version has more than one answer.

Tandem mass spectrometry with fragmentation gives sequence information that intact mass cannot. It is the analysis that would actually confirm identity, and it is rarely supplied.

Old habit: I write down the expected answer before I calculate it.

Building on post #73 rather than restating it.

Electrospray ionisation produces multiply charged ions. For a 4 kDa peptide you expect mostly 2+, 3+, and 4+ charge states. Reading an electrospray spectrum means recognizing the envelope, not looking for one peak.

If anyone has run this properly I would rather read that than my own guess.

Electrospray on a peptide of this size gives a multiply charged series rather than a single ion. Seeing only one charge state usually means the deconvolution has already been done for you, which is worth knowing.

I would want the raw data before agreeing with my own summary of it.

The honest summary of what a mass result buys you: it narrows the field of what the material could be, considerably. It never closes it, and no certificate should be read as though it had.

Correct me on the arithmetic if it is wrong; I would rather know.

Taking post #99 at face value and following it one step further.

An acylated peptide has a mass that reflects the modification, so comparing against the mass of the unmodified backbone gives a mismatch that is not an error.

If anyone can point at the primary source I would be grateful.

Taking post #110 at face value and following it one step further.

The honest summary of what a mass result buys you: it narrows the field of what the material could be, considerably. It never closes it, and no certificate should be read as though it had.