MS Method
MS Method tab in the MS Chromatogram window serves for setting up the MS Method.
Items in this section are common properties of all peaks defined in the MS Method and shown in the Result Table.
Sets the signal for the display in the Result Table. MS Result Table is the superposition of a standard signal (set in this field) and peaks defined in the MS Method Table. The default value is TIC signal.
Using the button invokes the MS Method - Peak Purity dialog used for defining the calculation method of Peak Purity value (as displayed in the Result Table).
MS Method - Peak Purity dialog
Restricts the comparison of the spectra only to the m/z range specified in the From and To fields to the left.
Defines the start and end spectrum for peak purity evaluation in % of the detected peak height. Available values range includes integer numbers in the range <0 - 100>.
Sets whether the calculations of peak purity value will be carried out based on All spectra or only the Five significant points (peak start, peak apex, peak end, both peak inflexion points).
The baseline (background) for individual m/z values is interpolated between peak start and peak end points. With the Use Background Correction checked, the spectra are measured against this surface.
Using the button invokes the MS Method - Spectrum Smoothing dialog used for defining the way how MS spectra are displayed - the available options are None, FFT Filter, Savitzky-Golay Filter and Moving Average filter. The last two allow to set the Window on which the smoothing will be applied - the higher Window value, the smoother the data will be. Side effect of such operation is increased noise and in some cases, shift of the spectral lines on the m/z axis.
MS Method - Spectrum Smoothing dialog
Sets whether the Conformity values in the Result Table will be calculated just from defined Reference m/z values or from the whole spectra. Calculating with the whole spectra is more precise, but also slower.
Allows to artificially lower the precision of calculating the m/z stick intensities and values. Default value is 0 (as in the data).
Allows to define the allowed imprecision of m/z values to be still considered in the same m/z stick.
Note:
In case the Centroid m/z Range is set to 1 (m/z sticks shown in the Spectrum Graph are with the e.g. 40, 41, 42, ...) and EIC Bandwidth [m/z] is set to 0.2, any spectrum containing data with 0.1 imprecision to the expected value will be considered as having that ion in. For example, any spectrum containing m/z line of 159.9 - 160.1 will be considered to have a stick of m/z 160.
Sets the value of maximal error in spectra conformity calculations. This value is used in the Result Table for the calculations of Conformity and also for relative Intensity of reference m/z ions.
Sets the tolerance of the peak maximum position so that the peak found on the Result Table Signal is matched to a peak as defined in MS Method Table. The value is defined as a percentage of the Left Wnd and Right Wnd compound property, as defined in the MS Method Table. Default value is 10 %.
This section serves for creating and maintaining calibration files from already filled in MS Method.
Using the button creates a new calibration file and fills it with information already entered into the MS Method table. Columns being filled in in the MS Calibration file
The button is only active when a calibration file is already connected to the MS Chromatogram. Pressing it updates the calibration file with compounds which are present in the MS Method but not in the calibration. Compounds already present in the MS Calibration file get the information in the Quantified On, Reten. Time, Right Window, Left Window and Peak Selection updated. In certain situation (when using Best Match in Peak Selection or Weighted EIC Sum in Quantify On) spectral information is required and it is updated as well. The responses and amounts of those compounds are not influenced in any way. Compounds present in the calibration, but not in the MS Method table, are not influenced in any way.
The button is disabled when MS Chromatogram is opened with Stored MS Calibration and tooltip is displayed next to it.
Displayed tooltip for Stored MS Calibration
Serves for setting the subtraction chromatogram (most probably the blank) for signal subtraction. No scaling or moving of any data points is performed, just simple subtraction.
Section defining the way how spectra are displayed in the spectral graph. The user may want to display the spectra in the Stick Spectrum mode or in the Raw Spectrum mode. The display options for both modes are set in the Graph Properties - MS Spectra dialog, accessible through local menu of the spectrum graph.
Using the button invokes the MS Method - Peak Detection dialog used for defining of the MS Spectra peak detection mechanism:
The mechanism is simplified peak detection mechanism only using two parameters for the whole spectra - Noise Threshold and Peak Width. Both parameters are set using sliders.
Sets the noise threshold for the detection of the peaks - the higher the value, the less peaks will be detected in the spectrum.
Sets the peak width parameter for the detection of the peak. This value is dependent on the spectrum precision of the MS detector - the denser the spectra are, the better peak detection can be achieved. Higher values of Peak Width will cause in fewer peaks detected.
Note:
While setting the peak detection parameters, it is necessary to be careful. Wrong settings may invalidate any stick representations of the peaks, among other things (sticks representing the peaks in spectrum will be clearly off if wrong parameters are set).
The table defining the MS Method parameters. Rows in the table correspond to compounds of interest, columns hold the information for particular compound. It is possible to add the compounds into the table either manually (by editing the last empty row) or by using the Single Compound Search 
andAutomatic Compound Search 
functions from the MS Menu.
Shows the name of the compound in the MS Method. The name is by default taken from the MS Library if the user uses the library search, but can be changed. No two rows of the MS Method Table can have the same Compound name.
Defines the link to the library if the MS libraries are used in the Extension. The link is defined by the Library name and compound ID. In case no spectral libraries are used, the Library column will be empty and the ID will be set to 0 for particular compound.
Note:
The columns are colored yellow in case Raw spectra are displayed (no library spectra are worked with in the Raw Spectrum mode), or the cells on a row may be colored red to warn the user that the compound with the ID as set in Library Compound column is not available in the library defined in the Compound column, or that the library itself is not at the expected place.
Defines on which signal will the particular compound be quantified. The option are TIC, any of the four reference extracted ions (EIC1..4), EIC Sum, Weighted EIC Sum or any standard signals defined in the method (either from the MS detector or from external detector). The default option is EIC1.
Note:
Spectrum and spectrum related information are necessary for using Weighted EIC Sum.
Columns for setting up the reference m/z ions for compounds in the MS Method Table. The values for m/z ions may be entered either manually or interactively using the Add Reference m/z function from the MS Menu
This section of the MS Method Table serves for setting the areas of the chromatogram where the given peak will be searched for. The meaning of the Ret. Time, Left Wnd and Right Wnd is the same as described in the Calibration Table of the Calibration window - they define the expected peak retention time and a span to lower and higher retention times, respectively, to search for the peak. Peak Sel. column (hidden by default) means peak selection and defines which peak will be taken if more than one is found in the time interval on the quantification signal - the options are peak Nearest to the expected retention time, First peak in the interval, Last peak in the interval, Biggest peak in the interval (based on Response Base settings in the MS Calibration) and the peak with the Best Match of it's spectrum to the expected library spectrum that is in the interval. Nearest is the default option.
Caution:
Left Wnd and Right Wnd define the search interval on the quantification signal which is specified for compound. When two (or more) compounds are quantified on the same signal and their Windows are set in a way they would overlap, the Windows are shorten so no overlap happens. On the other hand, Windows of compounds quantified on different signals do not influence each other in any way.
Mean Calculation section of the MS Method Table serves for defining how the spectrum of the peak which will be later used for spectral comparison with the library spectrum is calculated. The Calculation Type defines the means of the calculation, the Start and End columns the boundaries. The following Calculation Types are available:
None - a single spectrum from the peak apex is taken.
Relative [%] - spectrum being shown and compared is calculated as an average of the spectra in the interval from Start to End. The values entered into these fields are in percent from the peak beginning to peak end, -100 representing peak start, 0 peak apex and 100 peak end.
Relative - Peak Apex [min] - spectrum being shown and compared is calculated as an average of the spectra in the interval from Start to End. The values entered are times in minutes relative to peak apex - negative values mean retention time lower than peak apex, positive values retention time higher than peak apex.
Absolute [min] - spectrum being shown and compared is calculated as an average of the spectra in the interval from Start to End. The values entered are absolute retention times.
The default settings are Relative with values of Start of -10, End of 10. There are restrictions on possible values entered into the fields - basically the time entered into the Start column must be lower than the time in the End column for the compound. The values and Calculation Type may be filled in either manually by entering the values into the cells, or using the 
Set Mean Calculation Interval function.
Background 1 and Background 2 section of the MS Method Table serves for defining the background spectra used for subtraction from the spectrum of the peak. The subtracted spectrum is used for the comparisons with the spectral libraries and for the display. The Calculation Type defines the means of the calculation, the Start and End columns the boundaries. The following Calculation Types are available:
None - no spectrum is subtracted.
Relative [%] - spectrum being subtracted is calculated as an average of the spectra in the interval from Start to End. The values entered into these fields are in percent from the peak beginning to peak end, -100 representing peak start, 0 peak apex and 100 peak end. Values lower than -100 and higher than 100 are allowed.
Relative - Peak Apex [min] - spectrum being subtracted is calculated as an average of the spectra in the interval from Start to End. The values entered are times in minutes relative to peak apex - negative values mean retention time lower than peak apex, positive values retention time higher than peak apex.
Relative - Peak Start [min] - same calculation as for Relative - Peak Apex option, only the referenced time point is the peak start, not peak apex.
Relative - Peak End [min] - same calculation as for Relative - Peak Apex option, only the referenced time point is the peak end, not peak apex.
Absolute [min] - spectrum being subtracted is calculated as an average of the spectra in the interval from Start to End. The values entered are absolute retention times.
The default settings are None. In case both Background intervals are defined, the calculated spectrum is an average of the two background spectra, if just one interval is defined, the spectrum subtracted is fully defined by it. The values and Calculation Type may be filled in either manually by entering the values into the cells, or using the 
Set Background 1 Interval and 
Set Background 2 Interval functions.
Note:
Using the Background intervals will make the processing of MS chromatograms and work with them slower.