HP5972 MSD baseline below zero

[ontherun]

Hi All,

Our MSD HP5972 was recently serviced (GC is HP5890), the two filaments were changed, all works fine except that the baseline is below zero and so some of the peak's start and end times are below zero.
What causes this?
How can this be fixed?

Thanks

[asm]

Is the Tune/Tune Report ok? Have you done an autotune after the service?

[ontherun]

Yes, it looks ok, though I just did a "quick tune" not a standard autotune again (one was done following the service). EM volt was even lower than previous tuning 1765 vs 1812

[asm]

Can you take a picture of the issue and eventually one from before?

Is the baseline below zero at the online signal or in data analysis too?




From curiosity: Which software do you use and what OS on your PC?

[ontherun]

The baseline is below zero in the online signal as well as in data analysis.
We use ChemsStation.

[ontherun]

any takers for my question?

[Don_Hilton]

What is your threshold for acquisition? If this value is too high, it will cut away baseline and the bottoms of peaks.

[Peter Apps]

any takers for my question?

What does the technician who did the service say about it ? - he has much more relevant information than the minimum you are giving us.

Peter

[ontherun]

Threshold was 150 in data acquisition and 100 in tuning but now both are at 100.

Also the baseline is only below zero when running samples of rather lower concentration as well as blank runs, this is, no injection or solvent injection only. For instance a 100 ppm sample vs. 500 ppm or higher, the baseline and start/end of peaks are visible in the 500 ppm run but not in the 100 ppm run.

[James_Ball]

There has to be some kind of subtraction turned on because an Electron Multiplier should never give a negative signal.

Do you see negative numbers if you are in manual tune while scanning?

Background Subtraction should only be available if you are running data analysis in the Parametric Retrieval mode.

Another possible thing to check is in Data Analysis under the Quantitate Menu, look at Edit Quant Report Options and see what the Y-Scale settings are, it could be scaling such that you are not actually seeing the baseline. I have had times when the lowest setting on the Y scale was 50,000 and anything below that just didn't show up. Set the TIC setting to 100 and see what happens.

[Don_Hilton]

Try setting the threshold in acquistion lower - perhaps even 10 or 0. What happens?

And how is peak size other than missing baseline? The reason for asking about the acquistion threshold is that it masks out very low signals and just substitutes 0 for numbers, allowing the instrument to write smaller data files. But if the overall sensitivity of the instrument has dropped or shifted, the baseline you are looking for may simply have low enough counts that it is not rising above the threshold.

[ontherun]

Thank you all for your replies. The issue does have something to do with the threshold setting as when I set it to match the setting in the tuning file (100), the baseline was visible.
However, it does some times get close to zero so the issue points out to what Don-Hilton is suggesting, I will try his suggestion next. Thank you.

[ontherun]

I did check on any background subtraction setting but there is not one. No, there are no negative numbers while tuning.
Good to know about changing the Y-scale in data analysis though the issue exists in real time data acquisition too.

[James_Ball]

I did check on any background subtraction setting but there is not one. No, there are no negative numbers while tuning.
Good to know about changing the Y-scale in data analysis though the issue exists in real time data acquisition too.

If you look at the bottom left corner of the live chromatogram window you will see the lower display setting. If that is above 0 then you will see problems similar to what you are seeing.

[ontherun]

Yes, that has been at zero all the time.