How to integrate mass spectral refenrence libraries into AMDIS

Recently, I got this question on how to import GMD mass spectral reference libraries into the Automated Mass Spectral Deconvolution and Identification System (AMDIS). As I think this might be interesting for other people as well, I copy the question and my answer below:

Hi, 

I am XXX in YYY lab at ZZZ university. I have just downloaded the following library GMD_20111121_VAR5_ALK_MSL.txt from  Golm Metabolome DB. Because I would like to use it AMDIS software.

However, the extension file of the library is in TXT and I need to converte it to MSL. I will appreciate a lot if you could tel me how to do it.

XXX

PS. I tried to rename the extention but it did not work in AMDIS

Dear XXX,

Thank you very much for using the Golm Metabolome Database (GMD).

Please use the Amdis software to convert the downloaded file into a library. I try to list all necessary steps in the following

• Open Amdis :)
• Click Library ==> Build One Library  (this option is only available if a data file is open)
• Click Files
• Click Load Library Select the file downloaded from the GMD, you might need to change file type to "all files *.*" to see your file with file extension .txt
• The import is now starting and as a result you should see a list of 2,594 imported spectra
• Click Files
• Click "Save Library As"
• Give a appropriate file location and name and use the file extension msl The file is now exported and a ".cid" file (compound identification library) is generated, this is a crucial step
• Click Exit to close the Library Window
• Click Analyse ==> Analyse GC/MS Data...
• Click Target Library
• Select Page "Libr."
• Select "Target Compounds Library"
• Click "Select New"
• Select the new generated file, not the file downloaded from the GMD Click Save Click Run

If you any problem with the library please don't hesitate to drop me a line.

Your feedback is highly appreciated.

Best regards

Jan

update spectral library for TargetSearch

Ricardo Silva pointed me to a problem in the GMD spectrum export for the TargetSearch software:

He wrote:

I've started to work with GC-MS analysis on R, and the TargetSearch recomends the golm database http://gmd.mpimp-golm.mpg.de/download/, but the librarys don't have Retention Index, is this correct? How do a get a library with Retention Indexes?

Indeed, I found a format error due to the globalisation which led TargetSearch fail to load the textfile.

Thanks Ricardo!

ps.: If you finde any problem, please drop me a line...

Tweaking ChemDoodle

Patrik Rydberg posted some code to automatically scale a molecule in the ChemDoodle canvas. I was looking for something like this for quite some time. Now I could this improve for my settings having molFile from many different sources by first scaling the molecule with the scaleToAverageBondLength(Number length) function.

See an example here:
http://gmd.mpimp-golm.mpg.de/Analytes/0a2b3536-2245-4c0e-bdbc-495766eeec67.aspx

My code (taken from Patrik) is below:

structure = ChemDoodle.readMOL(molFile);
structure.scaleToAverageBondLength(10);
size = structure.getDimension();
scale = Math.min(canvas.width / size.x, canvas.height / size.y);
canvas.loadMolecule(structure);
canvas.specs.scale = scale * .9;
canvas.repaint();


cheers

PubChem update

We regret that GoBioSpace service is likely to be unavailable today 17th. Jan.2012 on account of maintenance work and for the import of the current PubChem Compound and Substance databases. More than 2.5 million structures from the IBM BAO (Business Analytics and Optimization) strategic IP insight platform (SIIP) are now available in PubChem and we think this is very valuable for matching potentially unknown mass peaks.

Your GoBioSpace-Team

[update 2012/01/18]
We released a new data version of GoBioSpace, now including the latest version (yesterday, 2012/01/17) of PubChem Compound and Substance databases and adding 119,958 new unique formula to the GoBioSpace repository. However, approx. 190,000 formula are not referenced anymore and subsequently were purged from GoBioSpace.

GoBioSpace' depositors

GoBioSpace is a tool to turn measured masses into source tagged sum-formulas and with this blog entry I want to focus on the datasources.

new mass spectral library made available

Today I exported the current mass spectral library and linked the files on the GMD download web page.

severe bug in functional group prediction

Jan Lisec pointed me to a severe bug in the functional group prediction feature implemented in the GMD. It turned out that I normalised spectra before decision tree training different than spectra for spectral classification. Jan pointed me to a spectrum where the Phosphoric Acid Deriv group was predicted present based on m/z 299 although this particular mass had only a minimal intensity in this GC-MS spectrum.
The only good news is that the validation for the publication was not affected by this bug, because the cross validation is performed without this web interface. However, I removed this bug and want to apologise for this inconvenience.


Thanks Jan!

cheers,
the other Jan ;-)