Striking disagreement between precursor mzs in pFind and MaxQuant

[andrewjmc]

Hello,

In comparing search results, I have noted significant disagreement between m/z as reported by MaxQuant and pFind (Spectra.mass/Charge). I have confirmed this in two separate studies. Of note, the MaxQuant masses agree well with those reported by Dinosaur (through Quandenser).

Here is a plot of absolute difference (pFind - MaxQuant) in m/z across four Raw files (Orbitrap Elite) in FTMS/ITMS node:

The modal difference is -0.50286, the second most frequent is -0.67241, and the third -0.66997

In a second cohort (10 RAW files, Orbitrap Fusion), but with very few shared identified spectra, I see a similar phenomenon:

The modal difference is this time -0.50335

I'd be grateful for your advice as to why this difference may arise.

Many thanks,

Andrew