Analytics · Mass spectrometry

Reading an MS report that only gives you a single number — the long version

Analytics › Mass spectrometry mass error (ppm) counter-ion content LC-MS high-resolution MS

taper_tableTL3Regular21 Dec 2024#1

Reading an MS report that only gives you a single number — the long version — 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 semaglutide lot gives 99.1% purity. The supplier certificate for the same lot states 97.7%. 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?

25 likes 19mo

RidgewayTL3Regular12 Jan 2025 · edited#2

The opening post answers the question as asked. The question underneath it is different.

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.

4 likes 18mo

an.kirchnerTL228 Jan 2025#3

taper_table, post #1: Reading an MS report that only gives you a single number — the long version — 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 semaglutide lot gives 99.1% purity. The supplier certificate for the same lot states… Go to post

Calibration matters: a high-resolution instrument out of calibration can report mass with ppm error large enough to be uninformative. Check when the instrument was last calibrated before trusting the reported accuracy.

On balance I think that is right, and I would not bet much on it.

0 likes in reply to #1 18mo

Moved from HPLC & UHPLC by owen.brady. Category placement is not obvious from outside and getting it wrong is expected. This topic will get better answers here. The move is recorded in the public log citing R7.

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