Figure 3: “Display User Search Options” Window. Substructure Information After performing a User spectrum

After performing a User spectrum search, the hit list can be evaluated to produce substructure information. This can be obtained using the StructInfo Desktop Button or from the Substructure information selection on the Tools Menu. Both are active only when the Hit List Window contains the results of a User spectrum search. Selecting Substructure information from the Tools Menu or clicking on the StructInfo Desktop Button causes the hit list from the User spectrum search to be examined. The results of this examination are displayed in the “Substructure Information” Window. This Window contains information on the probability of the presence and absence of chemical substructures, an estimation of molecular weight, and an estimation of the number of atoms of chlorine and/or bromine that are present.

portion of the Desktop.

The Status Line is used to provide messages pertaining to the various selections on the option’s menus and the current display of the individual Windows of the Desktop. In addition, the status of searches is reported in the Status Line as well as the number of replicate spectra for hits that have replicate spectra.

The list of spectra in the Hit List or Clipboard Window is the active list. There is one and only one active list. The highlighted spectrum in the active list is the active spectrum. The active spectrum is the one displayed in the Plot, Structure, and Text Info Windows as well as the top spectrum in the Compare Window. The Previous Desktop Button is used to move the highlight bar up to the previous entry in the active list. It functions as the reverse of the Next button. It is only available when the highlight bar is not on the top entry in the active list. When the highlight bar is moved, the spectrum of the highlighted entry becomes the active spectrum and is displayed in the Plot Window, the structure of that entry is displayed in the Structure Window, the text data (synonyms, mass/intensity pairs, contributor, etc.) are displayed in the Text Info Window, and the spectrum of the highlighted compound is displayed as the top spectrum in the Compare Window. You can move up the active list with the Previous button. Like the Next button, this will move the highlight bar regardless of the active Window.

The Next Desktop Button is used to move the highlight bar down to the next entry in the active list. This entry then becomes the active spectrum. When a search is complete, the spectra found are put in the Hit List Window. The current contents of this Window are overwritten. The Next Desktop Button advances the highlight bar on the Hit List Window or the Clipboard Window to the next entry, depending on which Window contains the active list. The Window with the active list does not have to be the active Window. The Next button moves the highlight bar regardless of the active Window. If the highlight bar is in the Clipboard Window, selecting the Next button moves the highlight bar down to the next entry. If the highlight bar is in the Hit List Window, selecting the Next button moves the highlight bar down to the next entry in the Hit List Window. The button is only available if an entry exists below the highlighted entry. When the highlight bar is moved, the spectrum of the highlighted entry is displayed in the Plot Window, the structure of that entry is displayed in the Structure Window, the text data (synonyms, mass/intensity pairs, contributor, etc.) are displayed in the Text Info Window, and the spectrum of the highlighted compound is displayed as the top spectrum in the Compare Window. You can move up the list in either the Clipboard or Hit List Window by using the Previous button.

When available, the Repl Desktop Button is either ReplOn or ReplOff. The Repl Desktop Button is ONLY available when the highlighted entry in the Hit List Window has corresponding entries in the NIST/EPA/NIH Replicates Library, and the Replicate Library has been installed. If you select the ReplOn button when it is available, a list of replicate spectra appears below the highlighted entry in the Hit List Window, and the button turns to ReplOff. The origin of the entry is identified by (M) for spectra from the NIST/EPA/NIH Main Library and (R) for spectra from the NIST/EPA/NIH Replicates Library. As long as the NIST/EPA/NIH Replicates Library has been installed, the display of replicate spectra from a search is possible. This does not mean that the spectra in the NIST/EPA/NIH Replicates Library were used in the search. The hit for the highlighted entry is returned to a display of the spectrum from the NIST/EPA/NIH Main Library and any User libraries included in the search when you select the ReplOff button. Any other entries that have had NIST/EPA/NIH Replicates Library spectra displayed by selecting the ReplOn button stay displayed until the entry of origin is highlighted, and the ReplOff button is selected.

The UserSpec Desktop Button causes the “User Search Options” Window to be displayed. All nonautomated User spectra searches are performed on the highlighted spectrum in the “User Search Options” Window. A User spectrum search can be performed by double clicking on a spectrum in the Clipboard Window. The label for this Desktop Button is UserSpec when the search type selected in the “User Search Options” Window is Identity‑Normal. If a different type of search has been selected, the button label reflects the search type.

The StructInfo button results in the same action as the Substructure information selection of the Tools Menu.

The Constraints button displays the constraints currently available for use with various searches or the constraints associated with a current hit list generated from a search that used constraints. The function of this Desktop Button is similar to that of the Display Constraints selection from the Desktop Menu.

The AdjustWin Desktop Button calls a separate ”Adjust ...” Window for each of the seven Windows that make up the Desktop. You can change various attributes of the Windows. When you select the AdjustWin button, the “Adjust ...” Window for the active Window (the Window with the high-lighted title bar) is displayed. As an example, selecting the AdjustWin button with the Plot Window as the active Window causes the “Adjust Plot” Window to be displayed. You can adjust all the different colors for the various parts of the display as well as some of the features, such as the way the text data are displayed and whether structures are displayed with a spectrum. If you select Default from the Desktop option on the Menu Bar, all the program defaults for the Windows are restored. You can save your customized Windows with Save As selected from the Desktop option on the Menu Bar. The AdjustWin button is the only Desktop Button always available.

The QuickPrint Desktop Button sends output to the printer as defined in the “Choose Print Mode” Window. The “Choose Print Mode” Window is displayed by selecting Print from the File option on the Menu Bar. The last selected settings in this Window are used to define the output when you select the QuickPrint Desktop Button.

The sWitchBack button returns the display to the program from which the NIST MS Search Program was called. When instru-ment mass spectrometry data acquisition and reduction pro-grams allow for the launch of the NIST MS Search Program, use of this Desktop Button allows for easy return. This button is inactive (grayed) unless the program is called from within a manufacturer’s data system.

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  To grab a spectrum, put the Mouse pointer on the Window containing the spectrum to be removed. Click the RIGHT Mouse button. This will grab the spectrum. If the Window is the Clipboard or the Hit List, then put the Mouse pointer on the spectrum to be removed and click the RIGHT Mouse button. If you are grabbing a spectrum from one of these two Windows, you do not have to use the highlighted entry. The spectrum and its point of origin will appear in the Status Line on the bottom of the Desktop.
  

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  To discard a grabbed spectrum, move the Mouse pointer to the Trash can icon and click the RIGHT Mouse button again to complete the process. If the origin of the spectrum is the Plot, Text Info, or Structure Window and the spectrum is removed from one, it will be removed from all three. The entry for that spectrum remains in the Hit List and/or the Clipboard Window after it has been removed from the other Windows. If a highlighted spectrum is removed from the Clipboard Window, it is also removed from the three individual spectrum Windows (Plot, Text Info, and Structure). Spectra can be removed from the Compare Window without affecting any of the other Windows. The Trash can icon (at the lower right edge of desktop) is used in removing spectra from a Window.
  

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  To copy a grabbed spectrum to another window, move the Mouse pointer to that window and click the RIGHT Mouse button again. This is the only way to copy to the Clipboard Window a spectrum from the History List displayed in the Compare Window.
  

User Search Options Window

Details about the “User Search Options” Window are found by selecting the Window’s Help button.

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  Substructure identification – If the “Identify Substructures” check box is selected, each User spectrum search also results in the display of the substructure information. NOTE: The substructure identification is not instantaneous. This option is inactive (grayed) if the Automation/No Automation button displays Automation.
  

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  Automated batch searching – If the Automation/No Automation button displays Automation, all spectra imported to the Clipboard Window are searched when they are imported. Selecting the Automation/No Automation button causes the “Automation” Window, which is used to set the conditions for the automatic searches, to be displayed (Figure 7).
  

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  When performing a “Similarity” User spectrum search using the Neutral Loss or Hybrid options, selecting the Mol. Weight button causes an estimated molecular weight to appear. This can be changed by highlighting the number and inserting a new value.
  

You can search a group of spectra in the list box by highlighting them. The usual Windows conventions for selecting multiple items apply. After selecting the first spectrum of the list, hold down the key while selecting the last spectrum. This will select all spectra between the first and last. Multiple noncontiguous spectra can be selected by holding down the key while selecting each desired spectrum.

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  AutoReport On/AutoReport Off toggle button – If this button displays AutoReport On, the results of a User spectrum search are printed. The format of the printing is set in the “Automation” Window.
  

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  Penalize Rare Compounds - If this check box contains an "X", match factors for compounds present in few or no other databases will have their match factors reduced. This, in effect, leads to a relative increase in match factors for common compounds, roughly adjusting for so-called "a priori probabilities" of finding a compound in an analysis. This ONLY works for spectra in the NIST library.
  

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  “Pre-Search MW =” radio button and associated input field is filled with a molecular weight; the presearch considers spectra only of that molecular weight and ignores NIST Replicate library.
  

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  Limits On/Off – This button states whether m/z and/or abundance constraints are used. When selected, it causes the “Spectra Limits” Window to be displayed (Figure 6). This Window allows the entry of a peak intensity threshold, which limits peaks searched in the unknown spectrum (“Minimum Abundance:” Text entry field). It also has Text entry fields for “Maximum m/z:” and “Minimum m/z:”, which limit the range of peaks searched in the library spectra. Values in these fields are used only when an “X” is placed in the “Apply limits” check box. The Limits On/Off button reads Limits On when this check box is selected with an “X”. The Default button in this Window resets the values. The “Spectra Limits” Window also has OK, Cancel, and Help buttons.
  

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  Automatic Search On – If selected with an “X”, it causes each spectrum imported into the Clipboard Window to be searched. The results for each search are stored and can be retrieved from the “Hit List History” Window displayed by selecting the  on the right side of the drop-down list in the Hit List Window.
  

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  Options button displays a Spectral Import Options window, which allows entering a linear m/z correction for the imported spectra and/or importing of the chemical name synonyms.
  

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  Return Focus to Caller upon Completion – This is inactive (grayed) unless the “Automatic Search On” check box contains an “X”. If the “Return Focus to Caller upon Completion” check box is selected, the display returns to the program that called the NIST MS Search Program. The spectra saved with routines in the mass spectrometer instrument data system can be imported automatically into the Clipboard Window when these programs are used to call the NIST MS Search Program. The Automation/No Automation button in the “User Search Options” Window displays Automation On if “Automatic Search On” is selected.
  

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  Immediate Printing of Search Results – If this check box contains an “X,” each time a spectrum is searched using the User spectrum search, a report is printed regardless of whether or not the search is automatic. The AutoReport On/AutoReport Off toggle button in the “User Search Options” Window displays the status of the automated reporting. Automated report printing of a User spectrum search result can be controlled by selecting the appropriate check box in the “Automation” Window by selecting the AutoReport On/AutoReport Off toggle button in the “User Search Options” Window or from the File option on the Menu Bar.
  

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  Number of First Hits to Report – The default setting is 2, which means the first two hits and the unknown are reported in the printed output. If you include plots of the mass spectra in the report, three spectra per page are generated. The first page of the report contains the unknown spectrum and the first two hits. Subsequent pages have three library spectra on them. Each page and each hit are appropriately numbered. The printed report contains the name of the unknown spectrum as shown in the Clipboard Window and the InLib value shown in the title bar of the Hit List Window. Each identified hit is followed by the compound’s name. The formula, match factor (MF), reverse match factor (RMF), probability of the unknown’s and the hit’s spectra being from the same compound (Prob), and the hit’s CAS registry number also are displayed, as well as hit’s library name and ID number.
  

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  Include Spectrum Plots in Report – If this check box contains an “X” (default condition), the spectrum of the unknown and the library spectra of the specified number of hits are included in the report.
  

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  Draw Structures in Plots – If this check box contains an “X” (default condition), the report includes structures in the spectrum plots. This is inactive (grayed) unless the “Include Spectrum Plots in Reports” check box has been selected.
  

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  Apply Maximum Spectrum Length – If this check box does not contain an “X”, the m/z scale is based on the value of the highest peak in the unknown spectrum; if the check box is selected, the scale is based on the value entered in the “Maximum Spectrum Length” Text entry field. If a reported spectrum has peaks past the set value or past the maximum value set by the unknown spectrum, then the plot has an ► at the end of the m/z axis.