AMDIS Download Page

The Automated Mass Spectral Deconvolution and Identification System (AMDIS) is a computer program that extracts spectra for individual components in a GC/MS data file and identifies target compounds by matching these spectra against a reference library. It was developed at NIST with support from the United States Department of Defense and is freely available.

Available here is the current release of AMDIS (Version 2.65, February 2007 Release).

Starting from version 2.63, AMDIS uses a new Help file format; the CHM or compiled html help model. You can also download it separately below and examine it independently of AMDIS.

The Help file is also provided separately in PDF format; which can also be downloaded separately below.

As a new user to AMDIS you are urged to read Chapters 1 and 2 of the help in order to understand the basic features of AMDIS. Even if you know AMDIS already, you will find the tutorial style approach of Chapter 2 to be informative and very easy to follow.

Changes in AMDIS

This release of AMDIS (Version 2.65) has a number of minor improvements compared to version 2.64; primarily these have been requested by the users. Some bugs have also been fixed.

The improvements are as follows:

1. Multiple Scan Ranges - AMDIS now supports multiple scan ranges - that is different m/z scan ranges at different times in the chromatogram. Use Analyze/Settings/Scan Sets and put the Start and End time as well as the Low and High m/z for each scan set and then state the Number of Sets. Also use Analyze/Settings/Instr and select Use Scan Sets. For most cases this will not have a big effect, but it will help get better results for some cases where the scan range changes a lot from the beginning of the GC run to the end.
2. Component Width - The Component Width can now be a maximum of 32 scans on either side of the component maximum rather than 20 (set using Analyze/Settings/Deconv). However, it is not good chromatographic practice to have a high number of scans across an isolated peak. If the 10% points on either side have 8 scans between them, this is sufficient for good quantitative work and the signal-to-noise will be better with fewer scan across a peak. There are some cases where a specific component is very wide and increasing the component width may help in its analysis. However, it is generally better to first try reducing the scan speed used for acquisition to make the peak narrower; since more is not always better.
3. Retention Index Data - If you want to have retention index data calculated, but not used, set the Type of Analysis equal to Use Retention Index Data and the Maximum Penalty to 0 (set using Analyze/Settings/Deconv). The former, somewhat confusing method of getting this same result has been omitted.
4. Match Factor Penalty - There is now a "sudden death" cut off for the Match Factor Penalty (set using Analyze/Settings/Identif). The levels are now Weak, Average, Strong, Very Strong and Infinite and these correspond, respectively, to a 1, 5, 10, 20 and 1000 match factor point penalty per RI window. For example, if you set the RI Window to 10 and the observed RI differs less than 10 (ie, 1 window) from the library's RI value, there will be no penalty applied to the match factor. However, when the difference is greater than 10, there will a penalty of 1, 5, 10, 20 or 1000 per RI Window (ie, 10) beyond the 10. So for example, if the observed RI is 16 different from the library's RI value, there will be a 6/10 (=0.6) penalty applied; and so 0.6, 3, 6, 12 or 600 points. Since you start with 100 as a perfect match factor value, you can see that the Infinite setting will act as a very quick cut off.
5. Selection of Best Match Factor - There have been some algorithmic changes in how AMDIS selects the best match factor if you are not using Multiple Identifications per Compound (controlled using Analyze/Settings/Identif). Now if there are two or more match values that are large (>95), AMDIS will select the one that has the maximum area. This will more often identify the component that you think is the best.
6. Extra Width - AMDIS has always used multiple algorithms for areas and computes two values called Intgr. Signal (integrated signal) and Area. The Intgr. Signal value is the area under the component; where the latter can be seen graphically by right-clicking in the upper TIC window and checking the Show Component on Chromatogram menu item. However, there are alternative ways to assess a base line and these will sometimes result in the component's baseline being extended by one or more scans to one or both sides of the original baseline. This alternative area assessment is reported as the Area value and will be the same as Intgr. Signal, if no extension was determined, or otherwise will be larger. Previously there was no information reported about this alternative baseline, but now it is reported as Extra Width (in the Component section of the Informational Lists window). Its format is a-b; where, for example, 0-2 would mean that the baseline was extended by no scans to the left and two scans to the right of the original baseline.
   
   If you want to build a calibration table (external to AMDIS), you can use either one or the other area types, but do not mix them. We do not think that there is much difference between the two, but you may find one may be better for some types of analysis.
7. RT Analysis - You can now do an AMDIS analysis using library RT values as an alternative to RI values (set Type of Analysis = Use Retention Time). However, we still recommend the use of RI since there are extensive literature values for RI that can help you.
8. RI/RT Window and Match Factor Penalties - The RI/RT Window and Match Factor Penalties parameters (set using Analyze/Settings/Identif) are now automatically selected/cleared according to the Type of Analysis selected.

Note: Support for different column types in the Compound Editor used for a Target Compounds Library (MSL) has been removed. The reference to column type selection (previously set using Analyze/Settings/Identif) has correspondingly been removed.

As always, we are interested in your comments and suggestions as to how we can make AMDIS a better tool for your use.

Download Section:

There are few types of downloads - select the ones that you need.

Other Versions

The version available at this site has been tested on these 32 bit versions of MS Windows: Windows 2000, Windows NT 4.0, Windows 95 or Windows 98. A 16-bit version and a "blinded" version (only information concerning identified compounds is shown) can also be downloaded. Contact the NIST Mass Spectrometry Data Center for further information.

  Download 16 bit version  

Download "Blinded" version

Earlier Versions

The first version of AMDIS was released September 1996 and has been distributed at no additional cost along with the NIST Mass Spectral Database since January 1998. It was also included as part of the NIST MS Database Demo package.

Searching NIST/EPA/NIH Mass Spectral Library

While users may develop their own target libraries, in order for AMDIS to search the NIST/EPA/NIH Mass Spectral Library, a copy of the current version of this library (NIST 02 or later) as well as the NIST MS Search Program (version 1.6 or higher) is required.  NIST Mass Spectral Library is available only from distributors. The NIST MS Search Program upgrades can be downloaded.

More Information

For a brief explanation of AMDIS and an overview of the program:

AMDIS Explanation

 AMDIS Overview 

The complete manual for AMDIS is available as a PDF file (link to download is above). It is also available as a Microsoft Word © document along with additional test data for AMDIS. The manual and sample data package are archived in a ZIP files, with additional instructions in a readme file. This data is supplied for use with the "Quick Start AMDIS" located in Appendix A of the AMDIS Help system.

Algorithms: Details of algorithms employed in AMDIS are described in the paper "An Integrated Method for Spectrum Extraction and Compound Identification from GC/MS Data" which appeared in the Journal of the American Society of Mass Spectrometry in Volume 10, 1999, pages 770-781. This paper is available in PDF format:

AMDIS Method Paper

The NIST MS Search Program v 2.0 can be downloaded separately.

Other Information

Overheads from Presentations

This page last updated April 17 , 2007