Chromatography Forum

Hello CF members, 5972 apparently tunes OK but baseline of a GCMS run starts below zero counts, becomes visible near end of chromatogram because of a little column bleed. This problem apparent from Standard Spectrum Autotune but not from Maximum Sensitivity Autotune, but of course the latter is weak on high mass ions. Ion focus seems high in both cases - 75v +. Plan to renew gas (He) purifier, then clean source; any other suggestions or experiences very welcome.

Mass Spec data should never give a negative baseline since the baseline value is the summation of the heights of all the mass spectra peaks in each scan.

Check in the Quantitation Report Options menu and see what you have the Y-Axis Scale set to. In the TIC under Minutes/Counts set it to just after your solvent delay and it should autoscale to the largest peak after that time. What may be happening is it is scaling with the minimum at some higher point than what your baseline is actually running.

Also in the main acquisition window look at the lower left corner and see if the value showing there is 0.0E0, if not then you may have a positive offset to the baseline which could be hiding it during acquisition. The arrows just above that box adjust the minimum counts displayed.

Thank you James for your attention. I am not obtaining a Quantification Report and the Y-axis settings are at default values i.e. 0 0 0. I presume that the QR is post acquisition, my problem is below baseline TIC in real time, despite apparently OK standard tune. Yes the Y axis minimum is set at 0.0E0.

Thank you James for your attention. I am not obtaining a Quantification Report and the Y-axis settings are at default values i.e. 0 0 0. I presume that the QR is post acquisition, my problem is below baseline TIC in real time, despite apparently OK standard tune. Yes the Y axis minimum is set at 0.0E0.

If you load the data file into Data Analysis do you see the baseline? Is it giving positive or negative height if it appears in Data Analysis?

What is the Threshold set to for the analysis? Could it be that the threshold is not allowing anything to be acquired at the first part of the run?

Data processing graphic below, showing "dropped" baseline

Maybe the "Threshold" needs to be set lower. On the TIC shown here, it looks like it's rejecting any ion signal below around 250 counts. (The Threshold is sort of like an "Area Reject" cutoff. It's found under MS Scan Parameters.) This can also happen if the EM voltage goes down.

Data processing graphic below, showing "dropped" baseline

Maybe the "Threshold" needs to be set lower. On the TIC shown here, it looks like it's rejecting any ion signal below around 250 counts. (The Threshold is sort of like an "Area Reject" cutoff. It's found under MS Scan Parameters.) This can also happen if the EM voltage goes down.

Data processing graphic below, showing "dropped" baseline

I am pretty well positive it is the threshold causing that. Try setting the threshold to 10 and see if you get more baseline. On mass spec if the detector doesn't see any ions above the threshold, then it draws a 0 baseline at those points, then you get the small spikes when some noise does come through.

Yes the threshold was set at 250; however replacing He purifier and just a quick tune seems to have abolished the problem. PF