Hello,
I'm putting the following conversation out, in the event other people wanted to do something similar, and find it helpful.
n.b. AMDIS reads datafiles from a lot of vendors (not just Agilent).


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Hi Alex,
I am not sure, if is possible!
My idea is : I have a mass-spectrum from a active run and I will search this spectrum in other 100-500 gc-ms runs !!
I want see in which runs, I had this compound….
Is it possible?
Thanks
Yuecel
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Betreff: Re: Macro !

Hi Yuecel,

too easy, you don't even need a macro to do this :-).
there is an excellent programme called AMDIS.
and its' FREE, follow the links at http://www.amdis.net/

the trick is to learn how to use it, and I can guide you, (as
the user manuals are not straight forward to understand).
I strongly recommend learning it, as it is a very powerful tool !. and makes life easier.

Q) do you have Excel or similar spread sheet programme (openoffice.org)?

So what you'll be doing in AMDIS is :
1)loading the data file with the mass spectrum you want to use.
2)selecting the mass spectra
3)getting AMDIS to make a new Library, containing only that single spectra.
4)go to settings, and select the new library with that single spectra, and save.
5)go to batch reports,
6) load all the data files you want to search.(select a couple to begin learning on, as the data processing may take up to a couple of minutes per file, depending on size, and number of compounds in it, etc...)
7) save the batch job, remember where you saved it !!!!!!!!
8) run the batch. and wait until finished.
9) I suggest the following.
a) go to where you saved the batch job in (7)
b) you will find also a tab delimited text file with the same name there. (extension .TXT)
c) right click on the TXT file, and select "open with", and choose Excel.
d) Excel will open up and display what files had library matches,
e) their quality of match is titled 'net'
f) using excel, select all, and use the data sort function.
g) select 'net', and click on 'descending order', so that the spreadsheet will display the best matches first.

now go back to AMDIS, click on the files of interest, in the dialogue box that was opened after the batch was run.

N.B. if you click on a file that didn't have a library match, AMDIS will revert to component view, simply go to 'Mode','target mode', so that it displays the library hits for that data file again. (its annoying as you'll find out, but AMDIS is so powerful)

If you used retention time locking, for your runs, you can also use retention time to sort further, if the spectra isn't unique., and/or have multiple compounds in the library, and sort by 'name' then 'net' too. the possibilities are vast.

So you end up with a list of runs which had the compound :-)
, all without printing out a single piece of paper, reading hundreds of text files or opening manually hundreds of datafiles.

regards
Alex

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Betreff: RE: Macro !
Dear Alex,

it is runing…! Can I do this procedure for more than one spectrum in the library?

Thanks
Yuecel

-----Ursprüngliche Nachricht-----
Betreff: RE: Macro !

Hi Yuecel

Yes,
I'm sorry that wasn't clear when I wrote

"and/or have multiple compounds in the library, and sort by 'name' then 'net' too"

I was trying to keep it simple so as to not confuse anyone.

I'm glad to read that you have it running, I hope you enjoy using AMDIS, and make sure you tell your friends :-),
there are heaps of other functionality it can do, (except integrate peaks to give an area)
and the sweet ability to compare two chromatograms and display compounds that are in one, and not the other.
which maybe applicable to your work if your trying to find trace contaminants in a product from one batch to the next.

regards

Alex

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