MS/MS sequence confirmation: what it costs and when it is worth it

MS/MS sequence confirmation: what it costs and when it is worth it — setting out what I have, and where I think it stops being reliable.

I would like to understand what this number means before I repeat it anywhere.

A PeptideMeter report on a retatrutide lot gives 98.4% purity. The supplier certificate for the same lot states 99%. Both documents name a reversed-phase method; neither states the same gradient.

My question is not "who is right". It is: given that those two figures were produced by different methods, what is the largest difference I should expect from method alone, and at what point does a gap stop being explainable that way?

Picking up the opening post: that is the part I would want checked first.

Thank you for the correction. I have edited my earlier post with a note rather than silently, so the thread still makes sense to read. The error was mine and it was the kind that comes from remembering a figure instead of looking it up.

Sample matrix effects: if a sample is dissolved in a complex matrix, other compounds in the matrix can suppress the peptide signal. Clean samples give higher sensitivity than dirty samples.

Quantitation by MS: most quantitation is done by LC-UV detection at 214 nm, not by MS, because extinction coefficients are better known. MS can quantify if an internal standard is used but that requires preparation.

Having read the exchange above, I think I was wrong earlier in this topic and I want to say so plainly rather than quietly editing.

The correction was fair and I had been repeating something I had not checked carefully enough.

Worth separating two things that post #3 runs together.

Resolution: "high resolution" commonly means <5 ppm across the mass range. Unit-resolution instruments achieve ±1 Da at best and cannot distinguish two species differing by less than 1 Da in total mass.