Chromatography Forum

Hello,

I am trying to view data files generated by our Bruker GC/MS in AMDIS. Although AMDIS can be set up for Bruker instrument and Varian data files (.xms) I cannot open my data files directly. I've been told that they require conversion to .xml format. I have been using the mzXML Conversion Utility to do this conversion. The resulting .xml files can then be opened in AMDIS. When the files are open and chromatograph shown, I cannot obtain spectra for peaks that were part of a SIM method. All of my data is collected in SIM and Scan simultaneously. Peaks that are not part of the SIM method can be clicked on and their respective mass spectra are shown. When I click on a peak that was part of the SIM method, I can only see one ion in the mass spec window. I know this situation is not specific to AMDIS as I have successfully opened my data files in OpenChrom and Insilicos as well. I have the same problem with my data files in these softwares. If I open a data file that was generated by a run done only in Scan mode, I can click on any peak to obtain the mass spectrum.

Is there a way that I can see the full scan data for the chromatograms that have both SIM and Scan content?

Thank you,
Rosie

Hi Rosie

SIM means Single (or Selected) Ion Monitoring - only one ion is detected and consequently there is no spectrum to display.

Peter

Peter has probably hit the nail on the head, but some systems allow you to set up alternate scans for scan and SIM. This is possible with the Scion. If this is the case it may be that the issue is in the conversion file which will not allow you to separate the alternate scans.

Check how you aquired the data.

Check your AMDIS version , why can't you open native XMS Varian/Bruker file types ?

Is AMDIS deconvolution compatible with combined SIM/Scan files from the Scion ?

You should try contacting your Bruker support people they should be able to advise.

CE Instruments,

AMDIS v.2.72 Jun 10, 2014 build should open the Bruker files. It has to do with the distributed dlls for various formats. This version of AMDI is distributed with NIST 14. If you don't have NIST 14, you should upgrade. I don't know if this version is available at chemdata.nist.gov or not.

Thanks everyone.

Yes, my system is capable of collecting both SIM and Scan data simultaneously in the same run. So when I open my data files in the Bruker software, I can view SIM and Scan data, separately, for the entire run. When the data files are converted for viewing in AMDIS, the SIM and Scan data seem to be combined.

I will look into the upgrade. Hopefully if the .xms files can be opened directly nothing will be lost in translation.

Thanks again!