Dear Sir. Concerning your issue about the possibility to subtract GC-MS chromatograms in MSD Chem Station. Yes, it is possible to subtract one spectrum from another and displays the difference. To subtract two spectra: 1.Select a spectrum (double-click the right mouse button in the

chromatogram). 2. Select the spectrum to be subtracted (double-click the right

mouse button in the chromatogram). 3. Select Spectrum/Subtract. The spectrum selected in step 2 is subtracted from the spectrum selected in step 1 and the resulting spectrum is displayed in window . To subtract background spectra:

1. Select a spectrum or average a range of spectra to subtract from the data file. 2. Select Chromatogram/Subtract Background (BSB). The system performs the following tasks: The selected spectrum is subtracted from every scan in the current data file. The subtracted data is stored in a BSB subdirectory in the same directory as the data file.The subtracted data file becomes the current data file and is displayed in window, For more details see the following below link and attached file which may help you in your analysis:

http://www.agilent.com/cs/library/usermanuals/public/G1701-90055.pdf

Thanks

Hi Bulat,

For the more experienced users, goto Tools | Options and select "Command Line" and "Stack".In the Stack windows you see X, Y, Z, T and R0 to R9. These are all "variables" where spectra and TIC or EIC chromatorams can be stored. Click on some spectra in a chromatogram to see how the Stack works.

You can do simple arithmetic like adding and substracting with the chromatograms (or spectra) stored in these variables, like substracting one chromatogram from another chromatogram (R1 = R2 - R3). You can do this in the command line. After he substraction you can use the DRAW command to draw the "new'"  chromatogram in one of the windows. Goto Help | Help Topics | Index tab to get help on how to use the DRAW command.

You can load one chromatogram (it will be in R0), store it in one of the Rx registers (R2=R0), load another chromatoram, store it in another registers. You have to play with it to get a good understanding of what you can do.

Good luck, Alex  

Hi Alex,

Thank you very much for very useful answer. This is exactly what I wanted.

Previously, I subtracted chromatograms in MS Excel after exporting 3-D Data. It was very time-consuming.

Best Regards,

Bulat

Hi Bulat,

Glad I could help. I even go a step further by reading the binaire data from data.ms directly to excel and manipulate the data before writing it back to data.ms (all using VBA macros).

You have to be an experienced programmer before attempting that.

Regards, Alex

Hi, Alex!

How do you work with data.ms files? They seem encoded. Our programmer uses CDF (NetCDF) files and Python for a software development. We have to export our data to CDF format.

Thank you!

Best Regards,

Bulat

Hi Bulat,

In the old paper manuals of I think the 5970/5971 HP MSD the binary format of the data.ms was fully described. That was maybe 20-25 years back. Although the format has changed a little bit, the storing of the spectra has stayed the same. I consider it to be a somewhat "open" format.

The data is not really encoded. Intensities are compressed in 2 bytes, masses are multiplied by 20 and everything is stored "backwards" (most significant byte first instead of last). 

Although I'm experienced with prgramming I'm not a real programmer. If you send me a private e-mail I can see if I can help you with directly reading the  data.ms files.

Regards, Alex

PS: I wish all GCMS manufacturers would publish the data format of there GCMS data or supply at least an API to access the data directly. 

Hi, Alex,

Thank you for the information and direction where to move!

I will discuss with our programmer what we can do.

Best Regards,

Bulat

Hi Bulat !

You can add or subtract. It's very easy.

See: http://www.mzgeochem.com/macros

Best regards

Daniel

Thank you, Daniel!

However, the software costs 200 Euros and is not available yet.

I almost finished my own software on Python to substract blank chromatogram from sample chromatogram. It just needs CDF files.

Dear colleagues,

Trial version of the Petrol Analysis software is available to any interested persons. The software allows extracting a lot of useful information from GC-MS data obtained after analysis of petroleum samples including concentrations of hydrocarbon groups and simulated distillation plots. The software has been actively used by Almaty Institute of Forensic Expertise for differentiation between different oil samples (cases on stolen oil, adulteration, oil spills, etc.). The software can also be used for the analysis of environmental samples polluted with petroleum hydrocarbons. Information about the software is available here: http://cfhma.kz/ecobio/en/petrolanalysis.html