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- Posts: 12
- Joined: Fri Feb 15, 2019 7:14 pm
Has anybody ever seen detailed documentation on the internals of the Chemstation tuning macros?
As part of my completely off-the-wall project for resurrecting a 5890/5971 I have developed a working program in python that can control 5971 MSDs for basic functionality - single scans, and acquisition of runs in scan mode. Modification to support 5972s and 5970s with SCII should be trivial. Adding SIM mode is a matter of finding the time to develop a SIM method and verify it.
However, any software to run an MSD is of no use if you can't tune the instrument. My software can use existing .U files to load tuning parameters but can't (yet) tune the MSD.
I am trying to reimplement the functionality of the 5970/71/72 tuning commands, and running into the following issues:
Both autotune and quicktune use built in commands 'simramp', 'axis' and 'abundance' which appear to be predefined internal functions in G1701AA and BA.
I have at least a suspicion of how 'axis' works based on the actual mass spec commands it issues. The same goes for 'simramp'. I have implemented neither functionality yet.
'abundance' is giving me major headaches:
Performing partial scans of m/z +-5 at 69, 219 and 502 and step 0.1amu with the calibration valve open results in a peak at 502 which looks very similar to what I see in Chemstation. For the other 2 ions, the resultant peaks look wildly different.
Basically, they seem to split 2 or 3 ways with very narrow peaks with a Pw50 of around 0.1 on the highest peak.
I'm pretty sure my initial tuning and scan parameters are the same as in Chemstation. The 5971 tunes fine in Chemstation and does not report any errors.
Adding a Savitzky-Golay filter to the output does reduce the splitting but adds other artifacts that aren't present in the Chemstation graphs.
Any ideas on what's going on here? Is Chemstation applying a particular filter to partial scans?