Commands:
Edit > Label Selected Peaks
Edit > Remove All Labels
Edit > Copy
View > Select & Scale
View > Zoom
View > Create Subview
View > Display Data
Spectrum > Display
Spectrum > Centroid
Spectrum > Calculate Protein Mass
Spectrum > Reconstruct Protein Mass...
Spectrum > Set Protein Mass...
Spectrum > Hide Protein Mass
File > Export > Spectrum...
File > Export > Spectrum Description...
Chromatogram > Display...
Chromatogram > Stop Reconstruction
Chromatogram > Centroid...
MS/MS Chromatogram > Show Matched Spectrum
Context Menu > MS/MS Spectrum
Context Menu > MS Spectrum
Spectrum > Calibrate...
A spectrum view displays spectral data.
There are three types of spectra: mass spectra, fragment spectra and chromatographic spectra.
Maneuvering within a Spectrum
Maneuvering within a spectrum is identical for all types of spectra:
- Zoom the x-axis: Mouse Down and drag below the x-axis
- Display full x-range: Double Click below the x-axis
- Zoom to a specific region of the spectrum: ⌥-Mouse Down and drag within the spectrum
- Display full y-range: Double Click left of the y-axis
- Display full y-range from 0: ⌥-Double Click left of the y-axis
- Display former range: Double Click into the spectrum (up to three former ranges are stored)
- Slide x-axis up resp. down: ⌥-Left Arrow resp. ⌥-Right Arrow
- Jump x-axis up resp. down: ⌃-Left Arrow resp. ⌃-Right Arrow
- Scroll spectrum view: Mouse Scroll horizontally and vertically
- Scroll spectrum view horizontally: ⇧-Mouse Scroll
- Using the scroller at the bottom of the document window scrolls the currently active spectrum
- Holding down the ⌥- key while clicking into the scroller at the bottom of the window zooms the spectrum around the current selection. If there is more than one selection or no selection at all the spectrum will be zoomed around its middle m/z value.
- A pinch gestures zooms the x-axis of the spectrum
Mass Spectra
There are two type of spectra, those that are alone-standing and those that are part of a chromatographic data set. In the latter case the spectrum offers an entry-port to the entire chromatogram.
Activities:
- Chromatogram generation: holding ⌥ ⌘ keys while click-dragging over a m/z range of the spectrum
- Measuring within the spectrum: ⌘ key while click-dragging over a spectral range
- Setting a selection: click-dragging over a spectral range
- Adding a selection: ⇧ click-dragging
- Labeling peaks: the command Edit > Label Selected Peaks labels the most abundant peak in every selection. Labels are editable.
- Removing labels: deleting their text removes individual labels. The command Edit > Remove All Labels removes all.
- Precisely define selections: command View > Select & Scale
- Magnify regions: the command View > Select & Scale
- Precisely define the displayed spectrum region: command View > Zoom
- Creating a spectrum from a range: command View > Create Subview
- Investigating data points: the command View > Display Data creates a table with all the data points covered by the selection(s).
- Display a spectrum of a defined time range from a chromatogram: command Spectrum > Display
- Calculate a centroided spectrum: command Spectrum > Centroid
- Calculate a protein mass from several multiply charged ions: the command Spectrum > Calculate Protein Mass calculates protein masses from the highest intensity points in the selections. At least two selections have to be set. The methods assumes that multiply charged ions are of the form (MProtein + nH)n+. Several protein masses can be calculated simultaneously but the selections for different proteins should not be intercalated.
- Reconstruct a protein mass spectrum: the command Spectrum > Reconstruct Protein Mass... reconstructs a neutral mass spectrum of specified range from the displayed range of the spectrum. The ions are assumed to have the form of (MProtein + nH)n+.
- Display multiply charged ions of a protein: Spectrum > Set Protein Mass... projects the location of multiply charged ions of the form (MProtein + nH)n+ onto the spectrum.
- Remove the projected multiply charged ions of a protein: Spectrum > Hide Protein Mass hides the projections
- Export a spectrum: the command File > Export > Spectrum... exports the spectrum in form of a tab separated m/z - intensity list.
- Exporting a spectrum description: the command File > Export > Spectrum Description... exports a spectrum description file. The spectrum description file encodes a general description of the spectrum quality - like the typical peak shape in a normalized form. If the current spectrum is derived from a chromatogram with fragment spectra the spectrum description file encodes two spectrum descriptions, one for the mass spectra and a second for the fragment spectra of the chromatogram.
- Copying the spectrum view: the command Edit > Copy copies the displayed spectrum view as a pdf-object to the clipboard.
- Calibrating a spectrum: the command Spectrum > Calibrate... starts a calibration work flow. Currently only 1 point and 2 point calibrations are supported. For a chromatographic data set all intact ion spectra use the same calibration.
- For All Ion Fragmentation (MSE) data: The context menu (ctrl-Click) command MS/MS Spectrum allows to display the fragment ion spectrum acquired at the same time.
The drag symbol


Fragment Spectra
Fragment spectra provide the same working environment like mass spectra only that they allow the generation of mass chromatograms only for datasets acquired in All Ion Fragmentation (MSE) mode.
Activities:
- Sequence views can be linked to fragment spectra to project the location of different fragment ions onto them.
- Calibrating a fragment spectrum: the command Spectrum > Calibrate... starts a calibration work flow. Currently only 1 point and 2 point calibrations are supported. For a chromatographic data set all fragment ion spectra use the same calibration.
- For All Ion Fragmentation (MSE) data: ion chromatograms from the fragments can be generated in the same way as for mass spectra.
- For All Ion Fragmentation (MSE) data: The context menu (ctrl-Click) command MS Spectrum allows to display the intact ion spectrum acquired at the same time.
Chromatographic Spectra
Chromatographic spectra are calculated spectra. The x-axis displays the time in minutes over which the chromatographic analysis was acquired. The y-axis represents an intensity value extracted from the spectrum acquired at the specific time. For the base peak chromatogram it is the highest intensity, for the total ion chromatogram it is the sum of all intensities and for mass chromatograms it is the sum of the intensities over a specific mass range of the spectrum at the specific time points.
Generally chromatographic provide give the same working environment as mass spectra only that instead of allowing the generation of mass chromatograms they generate summed mass spectra.
- Spectrum generation: holding ⌥ ⌘ keys while click and/or dragging over a time range of the chromatogram generates a summed spectrum of the covered time range
- Changing the type of the displayed chromatogram: the command Chromatogram > Display... allows to define precisely the type of chromatogram
- Stopping the reconstruction of a chromatogram: command Chromatogram > Stop Reconstruction
- Centroiding all spectra of a chromatogram: command Chromatogram > Centroid...
- Defining a norm-protein to normalise all protein quantities determined from this chromatogram to the quantities of this proteins: drag a protein-line from a Database Search View onto the spectrum
All Ion Fragmentation data sets allow the construction of chromatograms from fragments or from intact ions. Since no particular precursor is selected to generate the fragments a general question for All Ion Fragmentation data is: which fragment ions belong to a specific precursor and which precursor produced a particular fragment ion. This fragment - precursor assignments are based on their identical chromatographic profile.
If in a chromatographic spectrum generated from a particular fragment ion a peak is selected the command MS/MS Chromatogram > Show Matched Spectrum displays a spectrum of intact ions present at the time of the chromatographic peak. First, this spectrum is empty but it can be successively populated by peaks. The peaks are sorted according to their chromatographic profile. The peaks with the most similar profile appear first. Like this the precursor which generated the fragment ion can be identified. When selecting the chromatographic peak it is important to include the low-level environment of the peak so that this information is available for the chromatographic peak comparison.
The same procedure can be done in a chromatogram of an intact ion to find the fragments generated from this ion. Select a peak in the chromatogram of the intact ion and choose the command MS/MS Chromatogram > Show Matched Spectrum. A fragment spectrum will be displayed which first is empty but can be successively populated with fragment ions to find the fragment ions with the most similar chromatographic trace.