Chromatography Forum

Hello everyone,

I a currently working on a 7890B/5977A with turbo pump.

I try to run a SIM/SCAN method with 3 Groups SIM


time 0-6 : 64-96 - dwell : 100

time 6-19 : 43-55-70 - dwell : 100

time 19-22 : 43-67-68 - dwell : 100


When running the SIM/Scan method, only the first SIM group was collected. But looking at the screen of the acquisition software, each of the three group seems to be collected according to the method.

After the run, the SIM signal contain only the first group for all the run time

If we run only the SIM method with 3 SIM group - > all works and the three SIM windows were found into the SIM signal.

What we have done

- resend the firmware to GC and MS
- starting from a new method
-change the MS Mother Board
- change the network board
- change the sideboard PCA

The same 3-group SIM method works without any problem on an other GC/MS with the same configuration.

the software version is MAssHunter for acquisition : B.07.00 and data analysis F01.00

Lost ....

Thank you for your help

JFA

If you want, you can send me the raw directory: stanislav.bashkyrtsev@elsci.io, and I'll check if the problem is with the raw data. Then you'll know which part (the acquisition software or the one for offline analysis) to troubleshoot further.

Please, send us the raw data to: unichrom at unichrom dot com

New MS engine writes XML describing experiment setup, we can try reading it.
Maybe the excessive data confuses processing engine.
AFAIK in RAW directory lays all the scan matrix, SIM segments are selected in software just by summing specified regions.

Our UniChrom reads all the Agilent data formats
https://www.unichrom.com/chrom/uc-ffe.shtml
your example of multi-segment SIM can help us improve or file converter or advise you what to do with your raw data.


Thanks in advance.

AFAIK in RAW directory lays all the scan matrix, SIM segments are selected in software just by summing specified regions.

No, that would be an extracted chromatogram (aka EIC or XIC). SIM - is a special mode of mass filter, it's distinct from Scan mode. SIM dwells on a specific m/z longer and allows to gather higher quality information about specific ions.

It's possible to:
1. Set up SIM so that it switches between multiple ions, though not nearly as many as you'll get using Scan. As far as I remember Waters for instance allows only 32 of SIMs at a time.
2. It's also possible to set up instruments to gather one m/z over specified RT range, and then switch to another m/z at some point. This way if you know where your peaks are eluted, you can detect one m/z within one peak, and then another m/z in another peak.

What jfa-gc refers to is an experiment where there's both Scan Mode and SIM set up. This way you can gather high quality info about a specific m/z (e.g. for quantitation) and at the same time see what other m/z are present (for qualitative purposes).

And some instruments allow to use Scan mode and then automatically select highest ions and do SIM with them. This is called DDA - data dependent acquisition. Though usually I hear about it in the context of MS2, in which case it's actually MRM instead of SIM - but the idea is the same.

I have not encountered the problem with MassHunter B.10, but I know that B.07 would not support simultaneous SIM Scan with the 7000C GC/MS/MS, while B10 does. It may be something lacking in the software on the B.07 version that was fixed in later versions. You may need to contact Agilent to see if they issued a patch for that type of problem.