Automated Mass Spectral Deconvolution and Identification System (AMDIS) Software for Spectral Extraction and Compound Identification by GC/MS This software has been developed at the National Institute of Standards and Technology (NIST), an agency of the U.S. Department of Commerce, with the support of the Defense Threat Reduction Agency (DTRA, Department of Defense), to assist in the application of GC/MS methods for the verification of the Chemical Weapons Convention. It is available for general purpose use as part of the database software provided with the NIST/EPA/NIH Mass Spectral Database. The program has a brief tutorial that you can look at in the help file. This can be accessed either from AMDIS or by clicking on AMDIS_HELP.chm. The second chapter “Getting Started” can be examined to get a good idea of how to use AMDIS. We supply a data file in Agilent format (ALK3.D) for external calibration along with the calibration standards library (CSL) Alkanes.CSL. There is also a sample data file CARD5.D and an associated target library file (MSL) Pestplus.MSL. This file has some of the pesticides in the cardamom oil as well as some of the native compounds. Using these files along with reading chapter 2 will get you started with AMDIS very quickly. In addition, the program is provided with a few trial target libraries extracted from the NIST database. These are meant only as starting points for your own libraries. The libraries are relevant to flavors and fragrance analysis, toxic and environmental compounds and drugs as well as a small chemical weapons library. None have retention data. Help is available as a standard Windows help file, which may be accessed throughout the program. There is also a manual in the form of a PDF file (AMDISMan). QUICK GUIDE There is a brief guide called QuickGUIDE.rtf that will provide a step by step guide to your first analysis with AMDIS, including setting up the calibration file. It is very strongly suggested that you make use of retention indexing in your analysis. NEW FEATURES Depending on what version of AMDIS you have some of these may not be new to you. AMDIS now has the ability to filter data for components that were not identified by the target library. These filters allow you to automatically ignore low quality deconvolutions that often occur in highly complex matrices. In so doing the number of unidentified components will decrease and the overall quality of the data extracted for these unknowns will improve. Note, the filtering is only done after the target search, so no targets are ever lost. There is a new lower penalty level for RI - now you have the choice of Very Low, Low, Average, Strong, Very Strong and Infinite - corresponding to penalty levels of 1,2,5,10,20 and 1000 match factor penalty points per window. For some cases where you have good retention index data using a narrow window (say 2 or 3) and a Very Low penalty level will give correct identification for isomers. A bug that would from time to time crash the program while editing the library was fixed. FINAL NOTE We value your comments on what improvements can be made in AMDIS and many of the changes have come directly from user ideas. Dr. Wm. Gary Mallard National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 Internet: w.mallard@nist.gov