Spectrum Viewer/Analyser
The core of the mMass is Mass Spectrum module [Tools → Mass Spectrum] 
. This module is not a spectrum viewer only but provides some functions and tools for peaks labeling and spectrum analysis. The module layout consists of main spectrum window and control panel. In the control panel some additional information can bee seen, such as current cursor position (Cursor Info) or list of loaded spectra (Loaded Spectra), as well as a tool for peak searching (Find Point) and peak labeling setup (Peak Picking).
Mass spectrum viewer/analyser.
Spectrum navigation
Since most time in data interpretation is spent manipulating spectra (moving, shifting, scaling, zooming etc.), we aimed to make these functions as easy and user friendly as possible.
- Scroll spectrum - to scroll the spectrum use mouse scroll, [Left/Right arrow], [PageUp/PageDown] or drag x-axis with left-mouse button pressed. To jump to end of the spectrum quickly, press [Home/End] button.
- Zoom spectrum - to zoom a part of the spectrum select desired area with right-mouse button pressed.
- Scale x-axis - to continuously scale x-axis drag the axis with right-mouse button pressed, use mouse scroll with [Ctrl + Alt] pressed or use [Ctrl + arrow].
- Scale y-axis - to continuously scale y-axis drag the axis with right-mouse button pressed, use mouse scroll with [Shift] pressed or use [Up/Down arrow].
- Axis full range - to discard any zoom or shift double-click on appropriate axis.
- Spectrum full range - to see whole range of the spectrum double-click on spectrum with right-mouse button or press [Ctrl + Home].
- User defined range - to specify x-axis and y-axis range manually press [Enter] button and set the values in Spectrum Range dialog.
- View memory - to go to the previous view of the spectrum use [Backspace] button. This 50-steps view memory is especially useful during peaks labeling to temporarily zoom the peak.
View options
Some of the parameters of spectrum view can be set in Spectrum View Options dialog [Spectrum → View Options]. These parameters, however, are used for current document only. To set default view options use application preferences.
- Show label ticks - show vertical line representing peak intensity.
- Show labels - show peak label.
- Show annotations - show peak annotation too.
- Label angle - set label angle to 0, 45 or 90°.
- Show grid - show spectrum grid.
- Show legend - show names of loaded spectra.
- Show position bar - show current position within whole spectrum.
- Show gel view - show spectrum represented as a "gel".
- Gel height - set "gel" height in pixels.
- Show cursor tracker - show vertical line representing current cursor position.
- Show cursor position - show m/z value of current cursor position directly.
- Show cursor distance - show measured difference between two points directly.
Spectrum view options.
Peaks labeling
There are two methods available for peak labelling - Label Point [Spectrum → Label Point] 
and Label Peak [Spectrum → Label Peak] 
.
Label Point is the simplest method for peaks labeling. Using left-mouse button, selected point in the spectrum is labeled. Intensity value is interpolated from neighboring spectrum points.
Using left-mouse button and Label Peak tool, selected peak is labeled by centroid method with user definable height. The Height value can be set in the control panel. Intensity value is interpolated from neighboring spectrum points.
Delete label
Labels can be deleted using left-mouse button and Delete Label tool [Spectrum → Delete Label] 
or using Peaklist Panel tools.
Compare multiple spectra
To check any differences between mass spectra effectively, up to 9 additional spectra can be loaded simultaneously to currently opened document. To add spectrum, in the control panel press Add Spectrum button, use application menu [Spectrum → Add to Compare…] or drag spectrum file to list of Loaded Spectra (Mac version only). By double-clicking in the name in the list, spectrum can be renamed or shifted on y-axis. Spectrum can be temporarily hidden or removed using the list context menu.
Distance measurement
One of the most common tasks in mass spectrum analysis is a distance measurement of two peaks. This can be easily done using left-mouse button and Distance Measurement tool [Spectrum → Distance Measurement] 
. Measured distance is shown in the control panel and, if checked in the Spectrum View Options, the value is shown directly at cursor position as well.
More complex distance analysis is provided in Check Differences Tool.
Find point
To quickly search for specified m/z value in the spectrum, mMass provides a Find Point tool, located in the control panel. Just specify the m/z value and press [Enter]. Spectrum zooming can be also specified in Zoom combo. Set Current to use current spectrum zoom.