Precursor Mass Thermo RAW Files

[lutfia95]

Hi,

I am wondering, how are you correcting the mass of the precursor (m/z), I already checked the code part (Link).

The monoMz ("Monoisotopic M/Z:") is 929.9882
The precursor mass(isolationMzPossiblyWithOffset) from is: 930.3245239257812
Considering both, this will give a difference of 0.3363239257812438
iw ( "MS2 Isolation Width:") is 1.6
We don't use any offset so 0 and the scanDescription is empty. How/where is the correction afterward is made? the resulted number from msconvert is something like 929.9881......

Thx!
best

[chambm]

If the "Monoisotopic M/Z:" value is within the isolation window, it is used directly. No correction is made. There are a couple filters you can try to adjust the precursor m/z but they are rarely useful these days: precursorRefine and precursorRecalculator. Both only available from command-line.

[lutfia95]

thank you very much for your response! if the "Monoisotopic M/Z:" is not within the isolation window, is it corrected automatically? like the example above? I am interested in the correction method, if you could pin it to me in the code.

[chambm]

It falls back to the isolation m/z (the filter m/z retrieved directly from the API so it has more decimal places).