Application Layout
The application layout consists of several parts. Beside common parts like toolbar with selected features or statusbar showing current document information, main part is the document frame. On left hand side there is a Peaklist Panel - a list of all labeled peaks with values of m/z, intensities and annotations. Rest of the document frame covers currently active module with corresponding control panel on right hand side. In some cases, it can be very helpful to switch the document window to horizontal mode, with the peaklist panel bottom [Config → Peaklist Bottom] 
or to remove the panel completely [Config → Show Peaklist] 
to see the module frame only.
Main application layout.
Main menu
- File - common functions like Open, Close, Export or Print document.
- Peaklist - tools for peak selection, adding, removing, editing, copying etc.
- Spectrum - tools for peak labeling, comparing multiple spectra, view options etc.
- Processing - data processing tools like (re)calibration or spectrum crop.
- Matching - tools for matching of the data generated in Protein Digest Tool, Peptide Fragmentation Tool or the peklists from Compare Peaklists Tool to current spectrum.
- Sequence - tools for peptide/protein sequence editing and searching.
- Tools - main application tools.
- Links - links to the most popular on-line tools for mass spectrometry.
- Config - applications configuration tools.
Toolbar
Open Document - open existing document.
Save Document - save current document.
Close Document - close current document.
Print Spectrum - print current spectrum view.
Print Report - print current peaklist and additional document information.
Document Information - current document summary and user notes.
Mass Spectrum - spectrum viewer/analyser tool.
Sequence Editor - sequence editing tool.
Protein Digest - protein digest simulation.
Peptide Fragmentation - peptide fragmentation simulation.
Check Differences - search for specified differences between all the peaks.
Compare Peaklists - compare multiple peaklists with current document.
Label Point - label selected point in the spectrum.
Label Peak - label selected peak in the spectrum.
Delete Label - delete selected peaks in the spectrum.
Distance Measurement - measure distances in the spectrum.
Internal Calibration - calibrate data using internal calibration points.
Statistical Calibration - calibrate data using statistical calibration.
Add Peak - add new peak label manually.
Clear All Annotations - clear all annotations in current peaklist.
Delete All Peaks - delete all peaks in current peaklist.
Match Data - match data from active module to current peaklist.
Match Info - show summary of the latest match.
Annotate Peaklist - annotate current peaklist based on the latest match.
Mascot PMF Search - send current peaklist to Mascot server.
Mascot Sequence Query - send current peaklist to Mascot server.
Mascot MS/MS Ion Search - send current peaklist to Mascot server.
Modifications - set modifications to current peptide/protein sequence.
Search for Mass - search current sequence for specified peptide mass.
Search for Sequence - search current sequence for specified sub-sequence.
Import Sequence - import sequence from file.
Monoisotopic Mass - use monoisotopic mass for all mMass calculations.
Average Mass - use average mass for all mMass calculations.
Tolerance - set tolerance value and units for data matching.
- Show Peaklist - show/hide peaklist panel.
- Peaklist Bottom - switch to horizontal layout with peaklist bottom.
Preferences - application prefernces.
Statusbar
Selected information about current document are shown in application statusbar.
Application statusbar.