What is AMDIS:

• AMDIS is a new (easy to use) sophisticated software for GC-MS data interpretation from NIST.
 
Just imagine, you are a non-scientist  working with GC-MS.

You get the task to analyze some complex organic extracts. You are working together with one of the wonderfull technicans who prepare the samples and fill the autosampler for you - but you are responsible for the task - therefore you push the "START" button.

After more or less leisure you go home - free in mind - because on the next day AMDIS will also do the work for you. On the next day you start your PC and AMDIS - you load the files from the different systems to your desktop and press "Analyze". After some seconds you get a list with your target analytes (from some of them you never heard the name). You save the list and send it to your boss or customer. A day later you get your cheque.

Any problems (apart from the GC-MS and the cheque)?

Yes - because you are a scientist and have to verify your data. But AMDIS can help you to save time and to avoid the "mouse click syndrome" (from subtracting all your spectra manually).
 
 
 

 
• AMDIS can help you to analyze GC-MS data of complex mixtures, even with strong background and coeluting peaks. If you are working in SIM mode and you have external standards and want to quantify your compounds, you don´t need AMDIS. But if you have a noisy TIC spectra file and you want to find and identify known or unknown substances - AMDIS is the first choise.

• AMDIS  automatically extracts  pure (background free) component mass spectra from highly complex GC-MS data files and  uses these purified spectra for a search in a mass spectral  library.

• AMDIS can easy build library files from your own components and AMDIS will find these target compounds.  You can scan data files only for these specific compounds. (You don´t need to set "time windows" or such things - just click the analyze button)

 
• AMDIS can find substances under a straight baseline (of course if there are some). You don´t need to extract all the ions traces manually and in the time consuming way.

• AMDIS is free of charge with the omnipresent  NIST Mass Spectral Library package.

Never checked your CD? Never detected this nugget in your task list? Fly out and download the latest release for free.
 

What is this AMDIS not:

• After reading the text you may notify that this AMDIS is not that AMDIS (Association of Medical Directors of Information Systems)  nor that AMDIS  Atomic and Molecular Data Information System). (Read all the text and hate the joke? EMail me!)

• AMDIS is not a tool for quantification of GC-MS data.

How is AMDIS working:

• AMDIS analyses steps:  1. noise analysis, 2. component perception, 3. spectrum deconvolution, 4. compound identification.
 
First AMDIS analyzes the background and calculates a noise level for later processing. After that, it analyzes the data for an increase of a special ion trace. If there is maxima also for other traces at the same time, is assumes there is a peak and shapes a model peak. In the next step it calculates a "clean" spectra for each peak. And at last it identifies the compound via a library search.

Indeed its more complicated. You can read it in the AMDIS Method Paper:
"An Integrated Method for Spectrum Extraction and Compound Identification from GC/MS Data" by Steven E. Stein
 

AMDIS needs:

• For large date files with more than 100 substances: A Pentium-200 or better with Windows (for small data a Pentium 90 is ok)

• A user who knows a little bit about GC techniques and MS data evaluation, to avoid false positive and false negative identifications.

AMDIS can handle files from:

• Bruker
• Finnigan (GCQ, INCOS, and ITDS formats)
• HP Benchtop and MS Engines
• MassLynx NT Formats
• MicroMass
• NetCDF
• Perkin-Elmer
• Shimadzu MS Files
• Varian Saturn Files
• Viking

AMDIS download:

• download AMDIS free of charge at the AMDIS Download Page

AMDIS related Links:

the original sites from NIST

• AMDIS Home
• AMDIS Download - with the AMDIS Manual  and the AMDIS Method Paper
• NIST/EPA/NIH Mass Spectral Library

Tony Davies Column - an article by Antony N. Davies (ISAS Dortmund)

SIS Apllication Note - by O. David Sparkmann

NIST and AMDIS search - a little help file compiled by James L. Little

1999 IFT Annual Meeting Abstract 48-6 - Effect of salt concentration on the volatile composition of cucumbers fermented with a Lactobacillus plantarum culture that does not produce carbon dioxide from malic acid: R. F. MCFEETERS, C. S. Palma, H. P. Fleming, and F. Breidt

Article from Rapid Communications in Mass Spectrometry - Deconvolution gas chromatography/mass spectrometry of urinary organic acids - potential for pattern recognition and automated identification of metabolic disorders: John M. Halket*, Anna Przyborowska, Stephen E. Stein, W. Gary Mallard, Stephen Down, Ronald A. Chalmers

Comparison of gas chromatography pulsed flame photometric detection mass spectrometry, automated mass spectral deconvolution and identification system and gas chromatography tandem mass spectrometry as tools for trace level detection and identification - Shai Dagan, J.Chrom. A., 868, 2000, 229-247

• Mass Spectrometry on the Internet - a huge linklist compiled by D. Stöckigt (MPI Mülheim)
• sci.techniques.mass-spec home page - archive of discussion list
• MassLib - a powerfull tool for GC-MS spectra interpretation by MPI Mülheim/Ruhr, Germany (get the free DEMO-CD)
• MassFrontier - a powerfull tool for GC-MS spectra interpretation by Highchem Bratislava/Slovakia (get no DEMO-CD)
• GCQ2HP - my own (now a little bit useless) tool for converting Finnigan GCQ files to HP Chemstation files

If you have any questions, problems, annotations, hints, critics please E-Mail me.

- Who am I ?

kind@rziris.rz.uni-leipzig.de