Viewing Mass Spectra
AIA mass spectrometry data files also use the
extension .cdf. You may open them in the same
ways as chromatography files.
extension .cdf. You may open them in the same
ways as chromatography files.
The mass spectrum shows in the upper pane of
the split window. In most cases, there is a
sequence of mass spectra in the data, and upon
opening, the first scan displays. There is a stepper
to select which scan to display. If the data was
centroided, the spectrum shows vertical bars, if the
data is continuum, the spectrum is a line trace.
the split window. In most cases, there is a
sequence of mass spectra in the data, and upon
opening, the first scan displays. There is a stepper
to select which scan to display. If the data was
centroided, the spectrum shows vertical bars, if the
data is continuum, the spectrum is a line trace.
The lower pane shows either a total intensity
chromatogram (TIC) or an an extracted ion
chromatogram (XIC) derived from the sequence of
mass spectra. By moving the cursor in the ruler
across the chromatogram, you may select the mass
spectrum to be displayed. Similarly, by moving the
cursors in the ruler above the mass spectrum, you
may set the upper and lower mass limits for the
XIC. The Settings panel for the chromatogram lets
you select TIC or XIC.
chromatogram (TIC) or an an extracted ion
chromatogram (XIC) derived from the sequence of
mass spectra. By moving the cursor in the ruler
across the chromatogram, you may select the mass
spectrum to be displayed. Similarly, by moving the
cursors in the ruler above the mass spectrum, you
may set the upper and lower mass limits for the
XIC. The Settings panel for the chromatogram lets
you select TIC or XIC.
There is a variant of the AIA data format for
mass spectral libraries. In this case, the lower pane
shows a table of properties for each mass
mass spectral libraries. In this case, the lower pane
shows a table of properties for each mass
spectrum. By default, the table only shows the
name of the substance, but you may select other
fields using the Settings panel. Double-clicking on a line of the table will select the corresponding
mass spectrum. Similarly, selecting a mass
spectrum with the stepper will highlight its entry in
the table.
name of the substance, but you may select other
fields using the Settings panel. Double-clicking on a line of the table will select the corresponding
mass spectrum. Similarly, selecting a mass
spectrum with the stepper will highlight its entry in
the table.
By default, the mass spectrum is annotated with
mass values.
mass values.
The mass spectrum may have flags associated
with the data points. By default, these are not
shown on the spectrum display.
with the data points. By default, these are not
shown on the spectrum display.
Xhromatogram also allows multiple overlays on
top of the first mass spectra file. A stepper will
appear below the xic so you may select a file.
(Mixing chromatography files with mass spectrum
files may give unexpected results.)
top of the first mass spectra file. A stepper will
appear below the xic so you may select a file.
(Mixing chromatography files with mass spectrum
files may give unexpected results.)
The pane with the shaded frame is the "active data
view." The active data view receives commands such
as Copy, Unzoom, or Setings. Only settings appropriate
to the active data view will be presented. Clicking
in another pane switches the active data view.
view." The active data view receives commands such
as Copy, Unzoom, or Setings. Only settings appropriate
to the active data view will be presented. Clicking
in another pane switches the active data view.