I need to make more clear this message ... since we calibrate mz based on an offset + calculated error to set the second extraction tolerance its hard to say what it is here. (also the error message does not break down MS1 and MS2 ..)
Phase 2: Calibrate ....... WARN timsseek::processing::calibration: derived m/z window exceeded the first-pass window (15.0, 15.0) ppm; clamped. Residual MAD 4.2 ppm is contamination of the box-mean offset, not the instrument.
Probably the fix is to make a more elegant estimation of the error ... (rather than a mean fit a histogram and some form of density estimation fit ... maybe ...)
I need to make more clear this message ... since we calibrate mz based on an offset + calculated error to set the second extraction tolerance its hard to say what it is here. (also the error message does not break down MS1 and MS2 ..)
Probably the fix is to make a more elegant estimation of the error ... (rather than a mean fit a histogram and some form of density estimation fit ... maybe ...)