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Build database for AMDIS
Posted: Tue May 03, 2016 11:32 am
by Casimir
Dear all,
I contact you because I need to build a new database (.MSL) from 500 spectra. The format of the spectra is .MS and they can be read with AMDIS (chromatogram + mass spectra). I would build a database that I can use with AMDIS.
Please, do you have any advice for me to build quickly this database (.MSL) by using AMDIS ? There are indeed too many files to do this one by one.
In advance, I thank you sincerely.
Best regards.
Re: Build database for AMDIS
Posted: Tue May 03, 2016 2:00 pm
by carlo.annaratone
As far as I know, no other way to do it than by hand...
Re: Build database for AMDIS
Posted: Tue May 03, 2016 4:18 pm
by Casimir
Hi Carlo,
I'm really surprised that you can not do it faster... One of my colleagues has to do this job from 2 500 spectra (15 years of work); which does not to do this one by one !!
Re: Build database for AMDIS
Posted: Wed May 04, 2016 2:36 am
by chemstation
Can you please specify what format the .MS is, as I don't recognise it ?
As you mentioned that you want to create a NEW database. This suggests that you currently have a database with these 500 mass spectra in them and all you need as a conversion programme to convert from your current database into the .MSL format.
Re: Build database for AMDIS
Posted: Wed May 04, 2016 1:18 pm
by eselmeister
You probably could also try to use OpenChrom:
https://openchrom.net
Re: Build database for AMDIS
Posted: Wed May 04, 2016 4:40 pm
by Casimir
Hi eselmeister
I have OpenChrom (community Edition). However, I do no understand what method you use to build this database with OpenChrom...I would like to perform this operation at once (if possible) with my 500 spectra.
These spectra were acquires ten years ago by using a HEWLETT-PACKARD device. The format is .MS.
Thank you again !
Re: Build database for AMDIS
Posted: Wed May 04, 2016 9:26 pm
by eselmeister
Hi Casimir,
is the file called DATA.MS?
You could also send me a test file at:
philip (dot) wenig (at) openchrom (dot) net
or contact me via:
https://www.openchrom.net/contact
I would then try to find a way how to convert it to the AMDIS library format.
Best,
eselmeister
Re: Build database for AMDIS
Posted: Wed May 04, 2016 11:39 pm
by chemstation
It does appear that the .MS is an Agilent/HP chromographic data file, and not a single spectra file.
See Carlo's comment, as you need to do it one data file at a time, as AMDIS will invariably find trace peaks that will populate any library you automatically create.
If you spend an hour a day, doing 50 data files per day, then after 10 days
you will have your library.