NIST 17 MS Database and MS Search Program v.2.3 Page 17
been entered for any of these options, those values will remain until individually changed or deleted.
Once an available Constraint has been selected (check mark in check box entered by putting the
Mouse pointer on the check box and clicking the left Mouse button), the values previously entered for
that constraint will be used when a Constrained Search is performed. Because if a Constraint is
selected and is not visible in the Window, a bad result may occur, the program displays the number of
constraints selected. A Clear All button has been added to the Constraints tab of the Search dialog
box. The Clear All button removes the checks in the various constrains, it does not change the values
in each of the constraints. It is recommended to click on this button before starting a new Constrained
Search and reselecting any desired Constraints. Whenever any Constraint is selected, the Use
Constraints check box is automatically selected. Clicking on any individual Constraint’s check box in
the Constraints Window causes appearance of the Constraints tab of the Search dialog box to
change to allow for the entry (or edit) of values for that Constraint at the same time the Constraint is
selected or deselected. The appearance can also be changed to that for a specific constraint by
clicking on the constraint description away from the check box.
The last button on the right, the View substructure information button, displays the Substructure
Information dialog box. The Substructure Information dialog box contains a list of the probability of
the presence and absence of substructures that may be associated with a compound that produced
the searched mass spectrum along with additional predictions about this compound’s molecular weight
and estimate of the numbers of atoms of chlorine and/or bromine that may be contained. This is
especially useful with a Neutral Loss, Hybrid Neutral Loss Similarity, or MS/MS In EI Similarity
Search. An example of the use of Substructure Information resulting from an MS/MS in EI
Similarity Search of the EI Library is provided later in this manual.
Title Bar, Tool Bar, and Status Bar
At the top of the display of each of the Program’s tab is a Title Bar. The contents of a title bar of the
active tab are also displayed in the Title Bar of the Program Window. When the Lib. Search or Other
Search tab is displayed, this Title Bar will contain information about the currently displayed search. In
the case of a Library spectrum Search, this will include the search type used, whether or not
constraints were used, and if any type of limits were applied to the search. In the case of the Other
Search tab, the Title Bar will contain the type of search that was done (i.e., Formula, Molecular
weight, Any peaks, etc.) and whether or not constraints were used. When the Compare tab is
displayed, the Title Bar contains the number of spectra available for comparison regardless of the
number displayed.
At the bottom of the Program’s display, below the Program’s tabs, is the optionally displayed Status
Bar. The Status Bar’s display can be turned off by selecting or deselecting Status Bar from the View
menu. When a Library spectrum Search is being conducted, the left side of the Status Bar will have
displayed “Comparing XXX Library spectra with submitted spectrum” where XXX is the number of
spectra that were found during the Presearch (see Search Algorithms in Appendix 5). If Off has been
selected in the Presearch area of the Search tab of the Library Search Options dialog box, XXX will
represent the total number of spectra in the libraries being searched.
There are five fields on the right side of the Status Bar. The left-most of these five fields will have
displayed the selected search type in the “Spectrum Search Type” area of the Search tab of the
Library Search Options dialog box (Neutral Loss, Hybrid, or Simple if the Similarity Search is
selected; and Quick or Ident depending on whether a Quick or Normal Identity Search has been
selected).
The next four fields to the right of the box indicating the selected search type pertain to the currently
displayed search results. The first box to the right contains the type of search that was used in the
displayed search results. The next box to the right will have contained “Rev” if the Hit List is sorted
according to the Reverse Match value (the Match Factor obtained by ignoring all peaks that are in the
sample spectrum but not the library spectrum). To set this mode, select Reverse Search check box in
the “Spectrum Search Options” section of the Search tab of the Library Search Options dialog box.
The third box will contain the number used as a precursor MW value in a Neutral Loss or Hybrid
Similarity Search. If an Identity Search has been carried out, the fourth box will contain “Penalize” if
the Penalize rare compounds check box was selected in the “Spectrum Search Options” section of
the Search tab of the Library Search Options dialog box.