Changes in AMDIS

This release of AMDIS (Version 2.68) has a number of improvements; primarily, these improvements have been requested by the users and some bugs have also been fixed.

The improvements are as follows:

• Batch Processing – Batch processing has been improved. It is now possible now to assign different settings for the each task in the batch processing.
• Eastern Language Support – Support for eastern languages has been added. Names of the files will be shown correctly, if the operating system is set to support the language.
• MZXML Support – Support for the MZXML format is implemented. MZXML and MZDATA files can be analyzed if the files include mass spectral information.
• Process Larger Libraries – AMDIS can now process larger libraries. To aid in the clarity many small changes in output names have been made. Additional calculations for area are done. Many minor bug fixes have been introduced.
• Search Using Only Reverse Match – You can now search using only the reverse match (Analyze/Settings/Identif/ check "Only reverse search"). In addition SIM data is correctly processed (Analyze/Settings/Instrument select SIM under instrument type. Be sure to indicate the scan direction)
• Single Ion for Quantitation – It is possible to select a single ion for quantitation. In the Library Compound Editor put the m/z value you want to use to get areas in the box marked Ref. Ion. The program will then calculate the fraction of the total ion current deconvoluted for a component that is associated with this ion.
• Suppress Use of TIC – It is now possible to suppress the use of the TIC. For very complex chromatograms this can be valuable. To do so, select Omit m/z in the Analyze/Settings/Deconvolution and enter the value 0 for the mass.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

• 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.
• 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.