Nist standard Reference Database 1a nist 98 Mass Spectral Library with Windows Search Program (Version 7) For Use with Microsoft
From: C:\NISTMS\NIST$.EXE/V15/instrument To
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From: C:\NISTMS\NIST$.EXE To: C:\NISTMS\NIST$.EXE This command assumes the NIST MS Search Program is installed in the C:\NISTMS directory. C. Spectral Analysis Utilities for Users of NIST98 Automated Mass Spectrometry Deconvolution and Identification System (AMDIS) Included as a separate utility, AMDIS attempts to reconstruct original mass spectra for individual components in arbitrarily complex GC/MS and LC/MS reconstructed total ion current (RTIC) chromatograms and, if a target library is provided, ADMIS can directly identify target compounds. AMDIS is especially useful when an RTIC chromatographic peak repre-sents multiple components. Regardless of each component’s concentration, pure mass spectra are deconvoluted for analyses. AMDIS was developed by NIST for the Defense Weapons Agency (Department of Defense) for verifying compliance with a major international treaty (Chemical Weapons Convention), as ratified by the United States Senate in 1997. In order to meet the rigorous requirements for this purpose, AMDIS was tested against more than 30,000 GC/MS data files accumulated by the EPA Contract Laboratory Program without a single false-positive for the target set of known chemical warfare agents. While this level of reliability may not be required for all laboratories, this shows the degree to which the algorithms have been tested. AMDIS has been designed to reconstruct “pure component” spectra from complex RTIC chromatograms even when components are present at trace levels. For this purpose, observed chromatographic behavior is used along with a range of noise-reduction methods. AMDIS is distributed with specialized libraries (environmental, flavor and fragrance, and drugs and toxins), that were derived from the NIST98 Library. AMDIS has a range of other features, including the ability to search the entire NIST98 Library with any of the spectra extracted from the original data file. It can also employ retention index windows when identifying target compounds and can make use of internal and external standards maintained in separate libraries. A history list of selected performance standards is also maintained. The instruments that are supported in their native file format are: Bruker
Finnigan (GCQ, INCOS, and ITDS formats) HP Benchtop and MS Engines MassLynx NT Formats MicroMass Perkin-Elmer Shimadzu MS Files Varian Saturn Files Viking
In addition the NetCDF format which is supported by many manufacturers is supported. . Other formats will be added in future releases. Contact NIST for future information. MS Interpreter This new tool has been developed to aid NIST evaluators in their analysis of mass spectra. In one integrated program, it permits a wide range of calculations on a mass spectrum using—if available—a proposed chemical structure. Spectra and structures are associated in the library facility of the MS Search Program V.1.7 discussed above, and the program is activated from the Tools menu. Peaks in the spectrum originating as a logical fragment of the molecule are marked, and corresponding fragments may be highlighted. It also allows the analyst to keep track of important neutral losses, both from the parent or a derived ion and to compute readily possible formulas for any peak or neutral loss and isotopic patterns as desired. Observed isotopic clusters can be compared to theoretical predictions subject to a number of user-specified constraints.
From Program Manager, select File from the Menu Bar and then select Run from the File Menu. Assuming your CD-ROM drive is D, type D:\SETUP.EXE and select OK. If your CD-ROM drive is a device other than D, replace D with the appropriate drive letter. Follow the instructions presented by the SETUP program. Windows 95 or Windows NT 4 Select the Start button on the lower left of your screen. Then select Run from the Start Menu. Assuming your CD-ROM drive is D, type D:\SETUP.EXE and select OK. If your CD-ROM drive is a device other than D, replace D with the appropriate drive letter. Follow the instructions presented by the SETUP program. In upgrading from previous Windows versions of the NIST MS Search Program, Version 1.7 replaces the previous version of the Program and the Database unless the install directory is changed from NISTMS. Example Searches This section will describe several ways of retrieving and examining mass spectra. All searches of the NIST/EPA/NIH Libraries and User libraries can be initiated from the Search option on the Menu Bar. An explanation of each of the Search option’s selections follows. The Search Menu The Search option’s menu has the following selections: ID number Finds spectrum (or spectra) in selected library of having entered ID number (or range of ID numbers). CAS registry number Finds spectrum in NIST/EPA/NIH Main Library or User Libraries of a compound with CAS registry number entered. Chemical Name Incremental name search of the NIST/EPA/NIH Main Library or User Libraries. Name in User library Exact name search in selected User library. Formula Finds spectra in selected libraries of compounds with specified formula. molecular Weight Finds spectra in selected libraries of compounds having specified nominal molecular weight. Any peaks Finds spectra in selected libraries based on user‑specified peaks. User spectrum Searches user-defined spectra against selected libraries (a “library search”). Sequential method Searches selected libraries using a set of user constraints. This can be very slow. Search by Name If you have only a common or trade name of a compound and want to examine its mass spectrum, you can begin typing the name until it appears in the Incremental Name Search Window. Highlight or double-click the desired name, and the display in the Plot, Structure, Text Info, and Hit List Windows is refreshed with the appropriate displays for the compound. One of the Desktop displays provided (NameSrch.ini) is specially designed to implement the incremental name search. Select Desktop on the Menu Bar and then select NameSrch.ini from the five selections at the bottom of the displayed menu. To start a name search, click on the “Name” field at the top of the Incremental Name Search Window. To find the mass spectrum of a plant growth regulator, GIBBERELLIN A9, begin typing the name. Stop after entering each letter. After you have typed the letter N, you may scroll or page down the Window to see your target. The drop-down list box "Library" allows selecting a user library for the search. If the name of the library is not in the list, then its names should be indexed. This is a one-time operation. Select Tools on the menu bar, followed by Update User Lib Names… Select the user library you are looking for and click OK. Note the designation of the position where a molecular ion peak is, if one is present, by the triangle symbol on the horizontal axis of the mass spectrum. This appears in all spectra regardless of the presence of a molecular ion peak. Search by Any Peaks The Any peaks search became very popular when it was first developed over 20 years ago for use with the on-line Mass Spectral Search System from EPA and NIH. This has evolved into the powerful tool that exists in this version of the NIST Mass Spectral Search Program. Select Any peaks from the Search option’s menu. This will display the “Any Peaks Search” Window. The blinking vertical text cursor will be in the “m/z” field. “Normal” will be displayed in “Type” field. Type 82 and press Put the mouse pointer on the on the right side of the “Type” field and click the left Mouse button. Put the Mouse pointer on “Loss” in the displayed drop-down list box and click the left Mouse button again. This will cause the cursor to reappear in the “m/z” field. “Loss” will be displayed in the “Type” field. The first peak you are entering is an observed peak in the mass spectrum, and it is possible that it is the base peak. The second peak you are entering represents an ion formed by a loss from the molecular ion. Type 31 and press The next peak will be a “Maxmass” peak. Click on the on the right side of the “Type” field. Click on “Maxmass”. Type 303 and press Select the Search button in the “Any Peaks Search” Window. There are two Desktop configurations provided with the Program that are especially useful with the Any peaks search, LibNSrch.ini and LibSSrch.ini. The LibSSrch.ini Desktop configuration has only the Hit List and Spectrum Windows open. The Hit List Window is set to display structures. The LibNSrch.ini Desktop configuration has the Hit List, Text Info, and Spectrum Windows open. The Hit List Window is configured to display the names of the compounds that produced the spectra. In both of these Desktop configurations, it should be noticed that either an open or filled triangle is on the m/z scale of the spectrum. This locates the position of the molecular ion peak. The triangle is filled if a peak is present. Both the LibNSrch.ini and LibSSrch.ini Desktop configurations are useful with Molecular Weight, Formula, Sequential and ID Number searches. Library Search with a User Spectrum A User spectrum search finds spectra in the reference library that most closely match the submitted spectrum. Retrievals are ordered in the resulting “hit list” in terms of similarity to the submitted spectrum. The User spectrum search for this exercise uses a spectrum contained in the USERDEMO.MSP file provided with the NIST Mass Spectral Search Program. Select File on the Menu Bar, followed by Open. Put the Mouse pointer on USERDEMO.MSP in the “Choose Text File For Spectral Import” Window. Double click the left Mouse button. Select the Sel All button in the “Number of Spectra Found:” Window that is displayed. Then select the OK button. All the spectra in the file are displayed in the Clipboard Window. Use the Mouse pointer to highlight the fourth entry (Scan No 176 DEMO). This results in displays in the Plot, Text Info, and Compare Windows. Select the UserSpec Desktop Button at the bottom of the Desktop. This results in the display of the “User Search Options” Window. From the “User Search Options” Window, select the Search button. This carries out a Normal “Identity” search. The Windows of the Desktop will be updated. A special Desktop is provided for use with User spectrum searches: CmprSrch.ini. CmprSrch.ini has the Hit List Window configured to display text names, the Match Factor, Reverse Match Factor, Probability, and the source of the Library spectrum (Main Lib, Rep Lib, or a User library). This Desktop also has the Clipboard, Text Info, Compare with difference Windows open. Select Desktop on the Menu Bar and then select CmpSrch.ini from the displayed menu. Note the designation of the position of the molecular ion peak in the spectrum in the upper third of the Compare with difference Window. The structure shown on the top spectrum is associated with the Library spectrum. Depending on your display size and resolution, the structure may not be shown because of space limitations. You can change the Compare Window’s display by first making it the active Window, and then selecting the AdjustWin Desktop Button at the bottom of the Desktop. Change the selected display from “Two Spectra with Difference” to “Two Spectra”. In both views, the bottom spectrum is the user spectrum selected for the search. You can add a spectrum from the Hit List Window to the top of the Clipboard Window by double clicking the left Mouse button with the Mouse pointer on the desired spectrum in the Hit List Window. You can change the Hit List Window from a text display to a structures display by selecting the AdjustWin Desktop Button at the bottom of the Desktop and making the appropriate change in the resulting dialog box. Select the Structure radio button rather than the Names button in the View section of this dialog box. The NIST MS Search Program The Desktop 
Figure 1: The Desktop of Version 1.7. The appearance of the NIST MS Search Program’s Desktop is shown in Figure 1. The “Expanded Normal” view is the default for the Plot Window. This can be changed in the “Adjust Plot” Window and retained by saving the changed Desktop as one of the *.INI files using the Desktop option on the Menu Bar followed by the Save As selection on the Desktop Menu. The Desktop configuration in use when the program is exited is restored the next time the program is started. This Desktop configuration is stored as STARTUP.INI. Additional details can be found in the Help Screens associated with the “Adjust …” Window. Menu Bar File Option The File option on the Menu Bar has a Print automation selection. The default condition for this is a “check mark” at the front of the selection. This means each time a User spectrum search is carried out, a report is sent to the printer. Selecting Print automation in the File Menu removes the “check mark” and cancels the automated printing. Desktop Option The drop-down list box in the Hit List Window is a history list of all searches other than the incremental name search. A clear History List selection is on the Desktop option of the Menu Bar. Selecting this causes all the files that contain hit lists to be deleted and removes all entries from the “Hit List History” Window. Each time a search is carried out, the resulting hit list is stored as a file. You need to remove these files from time to time in order to free-up disk space. This is done by selecting Desktop from the Menu Bar and then selecting clear History List from the Desktop Menu. There is a Display Constraints selection on the Desktop Menu. When Display Constraints is selected from the Desktop Menu, a “Constraints Related Information” Window with a number of buttons is displayed. Some of these buttons may be inactive (grayed). The hit list related Constraints button is inactive unless the current hit list displayed in the Hit List Window is generated from a search where constraints were used. One set of buttons pertains to the program’s current settings, and the other set is for factors related to the current hit list. Each button in the set causes a separate display. The results of selecting the hit list related Constraints button is shown in Figure 2. If the current hit list is generated from a User spectrum search, the “Current Hit List’s Constraints” Window has a User Search Type button. Selecting this button results in the display of the “Display User Search Options” Window (Figure 3), which is the same display obtained by selecting either of the User Search Type buttons from the “Constraints Related Information” Window. 
Figure 2: “Current Hit List’s Constraints” Window. 
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