MS Search
MS Search dialog serves for setting the parameters for the search in spectral libraries. Clarity can perform three types of search - Single Compound Search, Automatic Compound Search and Target Compound Search.
Single Compound Search tab serves for performing a simple search of a single spectrum in one or more spectral libraries. It is invoked by using the Single Compound Search 
command from the MS menu of the MS Chromatogram window.
MS Search - Single Compound Search dialog
Either an exact retention time or an interval can be selected to search in. The values can be input manually or by selecting in the graph. The spectrum from the selected retention time will be compared with the spectral libraries and results will be returned based on further setting, i.e. Search Options and Background Subtraction.
When this button is clicked, a mouse cursor will be focused into the graph, where either an exact retention time can be selected by one click into the graph, or a range of retention time can be selected: while holding the CTRL key, first click into the graph to select the beginning of the desired interval, and second click into the graph to select the end of the desired interval.
Section allowing to set several parameters for the spectral search.
Restricts the hits returned to Clarity from MS Search program to just those with match factor higher than or equals to the value set in the field. Valid numbers are whole numbers from 0 to 1000.
Restricts the number of hits returned from the MS Search program to Clarity. Changing the value in the field only applies when the search is invoked again. Valid values are whole numbers from 1 to 100.
Sets the range of m/z values that will be searched in the library spectra.
- Search Only Selected performs the search using only up to four selected m/z values. Using this option searches the libraries only for spectra containing the selected m/z ions with non-zero intensities, giving best matches to compounds that have the relative intensities of such sticks closest to ones in the chromatogram.
- Search All But Selected excludes from the search up to four ions selected in the m/z 1..4 fields.
Note
When the Restrict m/z Range together with Search Only Selected are set, only those m/z ions belonging to this restricted range are searched.
Up to two backgrounds can be selected to be subtracted from the spectrum before the search. Such backgrounds can be input either as an exact retention time or as an interval.
When this button is clicked, a mouse cursor will be focused into the graph, where either an exact time for background subtraction can be selected by one click into the graph, or a range of time for background subtraction can be selected: while holding the CTRL key, first click into the graph to select the beginning of the desired interval, and second click into the graph to select the end of the desired interval.
When invoked, the search in NIST Libraries is performed using the external MS Search program. The MS Search being searched in can be set in the MS Search program (menu options Options - Library Search Options - Libraries tab), along with other search parameters.
Caution:
Parameters changes in the MS Search - Single Compound Search dialog will not be applied for results in the MS Search - Single Compound Search dialog until the Search or Preview Spectrum in Library button is pressed once again.
When invoked, the selected spectrum will be shown in NIST Libraries using the external MS Search program. More parameters can be set in the MS Search program (menu Options - Library Search Options - Libraries tab).
Caution:
Parameters changes in the MS Search - Single Compound Search dialog will not be applied in the search options in the MS Search program, manual search performed there may thus yield different results. To change parameters used for the search in MS Search program, Options - Library Search Options command must be used and changes must be done in the Library Search Options dialog (on various tabs).
Adds the checked rows from MS Library Search into the MS Method table.
This table contains the results of the search from the MS Search program. The table contains the Match, Reverse Match, Probability, Compound Name, Library, ID, Formula, MW and CAS No. columns, as used in the MS Search program.
The graph displays the overlay of the chromatogram signal as set in the Search In Ret. Time field used for the library search and the library spectrum of a compound selected in the MS Library Search table. Standard operations (zooming, etc.) are allowed in the graph, it's format (mainly peak tag format, overlay/head-to-tail mode, spectra colors) is dependent on the settings on the Graph Properties - MS Spectra tab. It is possible to open the tab using the context menu invoked by right-click in the graph area.
Automatic Compound Search tab serves for performing an initial search on a chromatogram where the user knows what he can expect. It is possible to quickly fill the whole MS Method table by running an Automatic Compound Search. The function is invoked by using the Automatic Compound Search 
command from the MS menu of the MS Chromatogram window.
MS Search - Automatic Compound Search dialog
Sets the signal on which the peaks will be detected and their spectra will be matched with spectral libraries. It is possible to select any standard signal including TIC, as well as external signals and signals extracted from the raw data (in such case you have to select the desired m/z in the appropriate field). While adding found compounds to MS Method, the signal set in this combo box will be propagated to Quantify On column in MS Method table.
By default the search interval is in the whole chromatogram. If needed, such search interval can be specified in the from and to edit boxes, enabled after unchecking the check box Whole Chromatogram. The spectrum from the selected retention time will be compared with the spectral libraries and results will be returned based on further setting, i.e. Search Options.
Section allowing to set several parameters for the spectral search.
Restricts the hits returned to Clarity from MS Search program to just those with match factor higher than or equals to the value set in the field. Valid numbers are whole numbers from 0 to 1000.
Enables to show up to 100 hits for each peak found in the selected interval of retention times (or in a whole chromatogram). Only the best match is shown, remaining results for each peak can be shown by clicking on the chevron in Expand column or by clicking on Expand/Collapse All Results check box. Only one compound per each peak can be selected .
Sets the range of m/z values that will be searched in the library spectra.
- Search Only Selected performs the search using only up to four selected m/z values. Using this option searches the libraries only for spectra containing the selected m/z ions with non-zero intensities, giving best matches to compounds that have the relative intensities of such sticks closest to ones in the chromatogram.
- Search All But Selected excludes from the search up to four ions selected in the m/z 1..4 fields.
Note:
When the Restrict m/z Range together with Search Only Selected are set, only those m/z ions belonging to this restricted range are searched.
Allows to select the libraries which should be used for the automatic search. It is possible to select multiple libraries.
Search
When invoked, the search is started and results are displayed in the MS Library Search table.
Note:
In larger libraries and on slower computers, the search may take several minutes to complete. A progress dialog is displayed during it's course.
MS Library Search table
This table contains the results of the search. The table contains the Expand, Chrom. RT, Selected, Match, Reverse Match, Probability %, Compound Name, Library, ID, Formula, MW and CAS No. columns and gives a number of best results for each peak found on a signal defined in the Use Signal field according to the Max Hits field. In case the search produces less results then the Max Hits value, only the found results are provided. By default, no peak has any library match preselected. It is possible to directly set the best match for the peak by using the Selected column checkbox on a given row or to display other matches and change the selection for each particular compound by the Expand column icon. It is also possible to use the Expand/Collapse All Results and Select/Deselect All Best Matches checkboxes modify the whole table instead just the single row.
Adds the checked rows from MS Library Search into the MS Method table. The Retention Time of the compounds in the MS Method table will be set to the times shown in the Chrom. RT field in the MS Library Search table, the name of the compounds will be set to Compound Name value from the MS Library Search table and can be later changed in the MS Method table.
Spectrum graph
The graph displays the overlay of the chromatogram signal as set in the Search In Ret. Time field used for the library search and the library spectrum of a compound selected in the MS Library Search table. Standard operations (zooming, etc.) are allowed in the graph, it's format (mainly peak tag format, overlay/head-to-tail mode, spectra colors) is dependent on the settings on the Graph Properties - MS Spectra tab. It is possible to open the tab using the context menu invoked by right-click in the graph area.
Target Compound Search tab serves for looking up the position or presence of the desired compound in the chromatogram. It is possible to quickly browse the spectra in the whole chromatogram and find the one with the best match with the spectrum of the target compound. The function is invoked by using the Target Compound Search 
command from the MS menu of the MS Chromatogram window.
MS Search - Target Compound Search dialog
Opens the Select NIST Compound dialog for selecting the desired compound. The selected compound is then displayed in the Compound: field.
Select the library to search in in the Library drop-down menu and type the name of the compound to search for into the Search field. The table below the field will restrict the available compounds in real time. Select the desired compound in the table and press the OK button to return to MS Search - Target Compound Search dialog.
By default the search interval is in the whole chromatogram. If needed, such search interval can be specified in the from and to edit boxes, enabled after unchecking the check box Whole Chromatogram.
Search
When invoked, the search is started and the result are shown in the MS Chromatogram Search.
This table contains the results of the search. The table contains the Chrom. RT, Match, Start Time and End Time columns and is filtered by Filter by Min. Match Factor slider.
Add Selected to Method
Adds the checked rows from MS Library Search into the MS Method table. The Retention Time of the compounds in the MS Method table will be set to the times shown in the Chrom. RT field in the MS Chromatogram Search table.
Move the slider to the right or left to change the intervals displayed in the MS Chromatogram Search table or input the desire value directly to the edit box next to the slider. The intervals are those in which all spectra have the Match of at least the value set on the slider. Moving the slider to the right (but still below the best match) will result in raising the number of intervals shown (in MS Chromatogram Search) as some particular spectra will not fall into the minimal match interval (they will split the interval to more than one), raising it even more will produce narrowing interval for the best match and later no interval displayed at all (as the Min. Match Factor will be higher than best match in the search. Moving the slider to the left will widen the interval and possibly add more intervals as similar spectra with worse matches will be available in different parts of the chromatogram too. It is important to set the slider for your search to a position where the interval shown is representative enough for the compound before selecting the desired one and pressing the Add Selected to Method button.
Spectrum graph
The graph displays the overlay of the chromatogram signal as set in the Search In Ret. Time field used for the library search and the library spectrum of a compound selected in the MS Library Search table. Standard operations (zooming, etc.) are allowed in the graph, it's format (mainly peak tag format, overlay/head-to-tail mode, spectra colors) is dependent on the settings on the Graph Properties - MS Spectra tab. It is possible to open the tab using the context menu invoked by right-click in the graph area.