There is no peak finding tolerance. There is only a PPM tolerance for chromatogram extraction in Centroid mode, which I wouldn't necessarily make lower than 10 ppm. You should use the View > Mass Errors > Histogram view to assess the actual mass errors in your data, and I would generally recommend a chromatogram extraction tolerance around mean + 3 * SD, i.e. if you see 1 PPM mean mass error and 2 PPM SD, then you could consider a 7 PPM tolerance.

Hope this helps.

--Brendan

Thanks, Brendan! and the Mass Errors Histogram is very useful!

BTW, how does peak finder logic work? does it pick the peaks with a PPM range with the highest signals? I've noticed that it picked some high tolerance peaks with higher signal over the highest dot products one with very tight PPM difference.

David