Re: peak lists m/z value difference generated by different software
Reply #4 –
pic3 looks like shoulder peaks. But difficult to see when I only have that zoom level.
What you need to do is take one of the largest peaks, look at the spectra, zoom in around the mass peak at low intensity. If you see a lot of small peaks (1-5%) around the real peak --> that is shoulder peaks and you need to filter them before an analysis.
0.0005 sounds too narrow to be to compare peak tables. 0.0025 seems more reasonable. The tools might choose the mass differently (at apex, mean/median across the peak, mean/median across samples).
16238 seems like a lot of features. Suggests to me something is up. Could be if there are many shoulder peaks, if you detect a lot of noise, or chop up peaks like mzmine did.
I am not familiar enough mzmine to tell you what to tweak but it makes sense if the other tools give you 1 or 2 peaks for that noisy peak.