The Compound View displays a list of all compounds available in the method (Compounds pane), all samples in the
current batch (Sample Results pane), and the peak plots for all compounds found in each sample (Sample Peaks
• Compounds pane
Use the Compounds pane to select a specific compound. The Sample Results pane displays all samples in the
batch and flags any sample that contains errors associated with the selected compound.
• Sample Results pane
Use the Sample Results pane to select a compound in a specific sample. The Sample Peaks pane highlights the
selected compound and displays the name of the sample in which the compound was found and the following
information about the compound: the chromatogram, retention time, area, height, and signal-to-noise ratio.
The Comparative View uses three panes to display a list of all compounds available in the method (Compounds
pane), all samples in the current batch (Sample Results pane), and the sample peak plots for all compounds found in
the samples (Sample Peaks pane) with the horizontal threshold guide.
The Comparative View uses the threshold method and amount that you specified in the method, the group that you
created on the Samples page, and the threshold sample that you selected on the Threshold Samples page to define
the threshold guide that it displays on the sample peak plots.
No error found in the selected
compound in these samples
Error found in the
in this sample
Horizontal guide indicates
the threshold value as
specified in the method.
The Qualitative View displays qualitative information for the selected sample. To see processed data for a sample,
you must select the Qual Processing parameter for that sample in the Batch View before you process the batch.
The Qualitative View displays a list of all samples in the batch (Samples pane), a list of all peaks in the selected
sample (Peaks pane), the chromatogram for the selected sample (Sample Chromatogram pane), the chromatogram
for the selected peak (Peak Chromatogram pane), the reference spectrum and spectrum data for the selected sample
(Spectrum pane), and the best library matches for the selected peak (Library Hits pane).
• Samples pane
Use the Samples pane to select a specific sample.
When you select a sample in the Samples pane, the associated Peaks pane displays all peaks found in the sample.
• Peaks pane
The Peaks pane works with the Samples pane to display graphical values for a unique sample and peak
• Sample Chromatogram pane
The Sample Chromatogram pane displays all peaks in the selected sample. The peak selected in the Peaks pane
displays a red marker.
• Peak Chromatogram pane
The Peak Chromatogram pane displays the selected peak.
• Spectrum pane
The Spectrum pane displays the reference spectrum from the library and the spectrum data for the selected
sample. The top pane displays the spectrum for the identified compound found in the reference library; the
bottom pane displays the actual spectrum data for the selected peak.
• Library Hits pane
The Library Hits pane displays the best library matches for the selected peak. Use this pane to select a different
library entry for the peak.
In the target screening display, the application displays a list of all samples in the current batch, the compound
results for all compounds in the method, and chromatogram and spectrum plots for all compounds found in the
currently selected sample.
The Target Screening View displays a list of all samples in the batch (Samples pane), a list of all compounds in the
selected sample (Compounds pane), the chromatogram for the selected peak (Chromatogram pane), and the
reference spectrum and spectrum data for the selected sample (Spectrum pane).
Use the Samples pane to select a specific sample in the batch. The associated Compounds Pane displays all
compounds in the method and flags any compound with errors in the selected sample.
Flags in the Samples pane indicate the following:
Reference spectrum from
Actual spectrum data for
A green circle means that the sample/compound/peak combination is identified and fully confirmed.
A yellow triangle means that the sample/compound/peak combination is identified but not fully confirmed.
A red square means that the sample/compound/peak combination is not identified.
Use the Chromatogram pane to display all extracted chromatograms of all adducts of the selected compound.
The first tab displays the most intense target adduct for the peak result. Additional (optional) tabs display extracted
ion chromatograms for other adducts for the target compound at the same retention time in order of intensity. If no
signal exists for an adduct, the first tab displays the XIC of the expected m/z within the specified retention and
chromatogram windows. When you do not specify a retention time or window, the application displays the full time
The Compounds pane displays all found peaks in the selected sample and flags any compound with errors. The
Target Screening Results grid reflects the identified compounds found in the compound database and the results of
the method processing criteria.
Use the Spectrum pane to display the spectrum, isotopes, fragments, and library search information for the selected
adduct in the Chromatogram pane. The Spectrum pane displays only the identification and confirmation criteria
specified in the method. The confirmations are based only on the most intense adduct.
The Spectrum pane includes the following pages of information (when available) for each selected
The application displays the neutral loss (NL) and compound/peak name information on the right side of the
Spectrum page. When data is available, the plot width is the full mass range in the raw data file. Otherwise, the
application scales the width to the scan range.
The isotopes page displays isotopic pattern results according to the threshold and deviation parameters defined
in the screening method. To identify or confirm the presence of a compound, the resulting score percentage from
isotopic pattern matching must be higher than the specified fit threshold percentage. An isotope peak is not
found if its intensity, relative to the monoisotopic ion’s intensity, is more than the specified intensity deviation
percentage away from the theoretical relative intensity of the isotope ion. An isotope peak is found if its
measured m/z is less than the specified mass deviation amount away from its expected m/z.
The Fragments page displays the maximum number of fragments as specified in the screening method. You must
define fragments in the screening library.
Expected m/z of the isotope
The Library page displays the matching library spectrum (in blue) and the experimental spectrum (in black).
The resulting score percentage from a library search match must be higher than your specified threshold value to
identify or confirm the presence of a compound.
The application scales both the matched library spectrum and the highest peak in the measured spectra at
100 percent intensity and displays the resulting neutral loss (NL) value for the matched library entry name to the
right of the plot.
In the unknown screening view, the application displays the following panes:
• Cross Sample Peak List Pane
• Heat Map Pane
• Sample List Pane
• Spectrum Pane
• Peak List Pane
• Peak Identifications Pane
• TIC Chromatogram Pane
• XIC Overlay Pane
• Group Averages Pane
• Peak Chromatogram Pane
• Cross Sample Peak Overlay Pane
• Library Search Pane
• Chemical Structure Pane
• Fragments Pane
• Isotopes Pane
Cross Sample Peak List Pane
Use the Cross Sample Peak List pane to compare peak values across all samples in a batch.
Heat Map Pane
Use the Heat Map pane to display the response of each peak occurrence in the batch. The Heat Map pane displays
all MS Area values for all peaks in all samples in the batch that are above the peak threshold value specified in the
method. When you select a peak in the Heat Map pane, the application displays the associated results for the
selected peak in all panes of the Unknown Screening view.
Sample List Pane
Use the Sample List pane to select a sample of interest. The application displays the associated results for the selected
sample in all panes of the Unknown Screening view.
When data is available, the plot width is the full mass range in the raw data file. Otherwise, the application scales the
width to the scan range.
Peak List Pane
Use the Peak List pane to select a specific peak found in the selected sample. The Peak List displays each peak that
the application identified in the sample.
Peak Identifications Pane
Use the Peak Identifications pane to display the name and formula for identified peaks and the source of the
TIC Chromatogram Pane
Use the TIC Chromatogram pane to display the relative intensity of a trace along the length of the sample data
Use the XIC pane to display the absolute intensity of an extracted trace along the length of the sample data retention
XIC Overlay Pane
Use the XIC Overlay pane to view specific groups of peaks. You can choose to view all peaks, selected peaks only, or
the top twenty most intense peaks (by area). The XIC Overlay plot is a collection of overlaid, extracted m/z ion plots
that use a different color for each peak.
Group Averages Pane
Use the Group Averages pane to compare the peak areas of different samples to a control group of samples.
Peak Chromatogram Pane
Use the Peak Chromatogram pane to display the selected chromatogram peak. The Peak Chromatogram pane
initially displays the apex scan for the detected peak. You can manually integrate the peak and use the updated peak
to generate reports.
Cross Sample Peak Overlay Pane
Use the Cross Sample Peak Overlay pane to compare instances of a selected peak across all samples in the batch. The
application overlays all occurrences of the peak in the batch. The application displays the names of all samples in the
batch where the selected peak is found. Samples that are assigned to groups are color coded, and the peaks found in
those samples are color coded in the plot.
Library Search Pane
The Library Search pane displays the best library matches for the selected peak, with the highest score listed first.
Documents you may be interested
Documents you may be interested