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msviewer - Explore mass spectrum or set of mass spectra

Syntax

msviewer(MZ , Y)
msviewer(..., 'Markers', MarkersValue)
msviewer(..., 'Group', GroupValue)

Arguments

MZ	Mass/charge vector with the range of ions in the spectra.
Y	Ion intensity vector with the same length as the mass/charge vector (MZ ). Y can also be a matrix with several spectra that share the same mass/charge (MZ ) range.

Description

msviewer(MZ , Y) creates a GUI to display and explore a mass spectrum, Y.

msviewer(..., 'Markers', MarkersValue) specifies a list of marker positions from the mass/charge vector, MZ, for exploration and easy navigation. Enter a column vector with MZ values.

msviewer(..., 'Group', GroupValue) specifies a class label for every spectrum with a different color for every class. Enter a column vector of size [numSpectra x 1] with integers. The default value is [numSpectra].

MSViewer GUI features include the following:

• Plot mass spectra. The spectra are plotted with different colors according to their class labels.

• An overview displays a full spectrum, and a box indicates the region that is currently displayed in the main window.

• Five different zoom in options, one zoom out option, and a reset view option resize the spectrum.

• Add/focus/move/delete marker operations

• Import/Export markers from/to MATLAB workspace

• Print and preview the spectra plot

• Print the spectra plot to a MATLAB Figure window

MSViewer has five components:

• Menu bar: File, Tools, Window, and Help

• Toolbar: Zoom XY, Zoom X, Zoom Y, Reset view, Zoom out, and Help

• Main window: display the spectra

• Overview window: display the overview of a full spectrum (the average of all spectra in display)

• Marker control panel: a list of markers, Add marker, Delete marker, up and down buttons

Examples

1. Load and plot sample data

   load sample_lo_res
   msviewer(MZ_lo_res, Y_lo_res)

2. Add a marker by pointing to a mass peak, right-clicking, and then clicking Add Marker.

3. From the File menu, select

   • Import Markers from Workspace — Opens the Import Markers From MATLAB Workspace dialog. The dialog should display a list of double Mx1 or 1xM variables. If the selected variable is out of range, the viewer displays an error message

   • Export Markers to Workspace — Opens the Export Markers to MATLAB Workspace dialog. You can enter a variable name for the markers. All markers are saved. If there is no marker available, this menu item should be disabled.

   • Print to Figure — Prints the spectra plot in the main display to a MATLAB Figure window

4. From the Tools menu, click

   • Add Marker — Opens the Add Marker dialog. Enter an m/z marker.

   • Delete Marker — Removes the currently selected m/z marker from the Markers (m/z) list.

   • Next Marker or Previous Marker — Moves the selection up and down the Markers (m/z) list.

   • Zoom XY, Zoom X, Zoom Y, or Zoom Out — Changes the cursor from an arrow to crosshairs. Left-click and drag a rectangle box over an area and then release the mouse button. The display zooms the area covered by the box.

5. Move the cursor to the range window at the bottom. Click and drag the view box to a new location.

See Also

Bioinformatics Toolbox functions: msalign, msbackadj, mslowess, msnorm, msheatmap, msresample, mssgolay

mssgolay

multialign

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