Chromatography Forum

Is there any way to get chemstation to subtract two TIC chromatograms to show me the differences between the two files?

Cheers
Damo

If you're in LC chemstation, I doubt it, because the file menu item "subtract background run", which you could otherwise have used (chemstation doesn't know whether it was really a background) doesn't work with MSD data.

However, you could just export the chromatogram to excel and do the job there.

Personally I am not a great supporter of this approach, because even the tiniest variation in retention time can lead to horrible ghost peaks. If a peak is absolutely identical in size and shape in two samples, but moves slightly to the left, you will get a narrow positive peak, and a narrow negative peak, at the start and end of the general area where the thing eluted. Worse, if the peak changes shape slightly (e.g. broadens), you can get two positive peaks either side of the proper RT, if you subtract the narrow sample from the wide.

You can overlay the TICs in Chemstation (or do the same with base peak chromatograms).

Thanks for the info

Thats what i normally do (overlay the TIC's) but i was looking for an easier way of removing peaks i dont want, i.e I've got a trace of a fragrance with a lot of isopar in, and i was looking at another way of removing the isopar without doing a background subtractions

Damo

there is free software called AMDIS from NIST,
and one of the nice things it can also do is compare two MS files,
it can highlight the differences between them, and into various categories, eg unique, larger in one than the other etc..., it is what I use when I am comparing two data files, and because it uses deconvoluted peak spectra, it isn't as susceptible to tiny RT shifts between runs.

Alex

Hi Alex

i've heard of amdis and it sounds good but can you use it with any library or is it only the nist that it works with?

Cheers
Damo

Damo,

Turn the filament off?...

Best regards.

AICMM LOL

Damo,

I am assuming you are running GCMS chemstation (G1701),
You can convert your MSD library to NIST library format, using
the Lib2Nist.exe from the NIST website

http://chemdata.nist.gov/mass-spc/Srch_ ... b2nist.zip

then setup NIST to include your library in its database search, then when you
send an unknown from AMDIS to NIST it will look in your Library too.

If the question is "how can I send all unique spectra to NIST to do library search" the answer is "I'd like to know too!", as at the moment I send one spectra at a time.

You can also make your own library in AMDIS, in the AMDIS format, that will be searched too when selected in settings.

Alternatively, I wrote a programme a while ago that does exactly what you want,
but it suffers from the slight retention time shift that occurs between runs.
it is called "File Subtractor"

http://members.dodo.net.au/chemstation/

in case you can't get AMDIS to run properly, though I strongly advise the use of AMDIS, to minimise false spectra.

hope this helps

Alex

Hi Alex

thanks for those ideas, i'll have a play around and see what results i get

Damo

aha! I just saved 2-5 days. Thanks all.