Commands:
File > Arcadiate Viewer
File > New Collection Window
File > Import
File > Export
File > Show in Finder
File > Recover from Validation Error
Window > Drawer
Window > Open Assistant
Window > Residue Library
Window > Isotopic Distribution
Window > Tasks
The command File > Arcadiate Viewer generates the main Arcadiate window. The window gives access to all the objects stored in its database and allows to create an arbitrary number of Data Collections - the environments to display and use mass spectrometric data sets and associated information.
The Library section gives access to imported data sets and to the Object Store.
Data is imported into Arcadiate using the command File > Import. Imported files populate one of the Library groups, Spectra, Chromatograms, Database Searches, Ion Groups or the Object Store.
The Object Store contains objects that are created in Data Collections and copied from there via drag & drop into the Object Store - for instance protein groups. From the different sections of the Library data objects can be dragged to Data Collections to be used there. Imported data objects are linked, not copied. Objects from the Object Store are copied.
When deleting imported objects from the Library they are removed from all data collections and deleted.
The command File > Show in Finder displays the data library in the Finder.
The command File > Recover from Validation Error deletes erroneous data from the Arcadiate database.
Pressing the button

The commands under File > Export allow to export a variety of content. The command refers always to the currently active view.
- > Spectrum Description… exports the spectrum description file. This file describes the characteristics of MS and tandem MS spectra and is required to import centroided data from the same instrument or type of instrument.
- > Protein Quantifications… export protein quantification results either as tab separated text, xml or MaxQuant proteinGroups file format.
- > Spectrum… exports a spectrum as tap separated text of a Spectrum View.
- > Precursors… exports the currently displayed precursor list of a Precursor View.
- > Ions… exports an ion group of an Ion Group View and its quantities as tap separated text.
- > Peptide List… exports the list of all identified peptides sorted by score of a Database Search Result View as tap separated text.
- > Proteins… exports the list of all proteins from a Protein Group View as a tab separated text file.
- > Molecular Markers… exports the list of all molecular markers from a Molecular Marker Group View as a tab separated text file.
- > Chromatogram as mzML… exports a chromatogram in mzML format. It is possible to export a chromatogram with non-identified fragment spectra only.
- > Database Search Result as xml… exports a database search result in xml format.
- > Fragment Spectra for Mascot Search… exports all centroided fragment spectra as a text file in Mascot Generic Format (mgf) for submission to a data base search.
The command Window > New Collection Window creates a new window similar to the Arcadiate Viewer which represents the currently selected data collection.
The command Window > Drawer displays the Drawer - a window with the hidden views of the currently selected Data Collection.
The command Window > Open Assistant displays the Assistant Panel - a panel with two sections: 1. information about possible actions in the currently active view and 2. the properties of the database object displayed in the currently active view.
The command Window > Residue Library shows the amino acid residue library that is currently in use.
The command Window > Isotopic Distribution shows a graphic display of the isotopic distribution of selected ions in a table which are linked to chromatograms. This window gives a rapid overview whether ions display the expected isotopic distribution or whether its peaks are overlaid with other ions. Peptide ions can be excluded on a per ion base from being considered for the quantity calculation of their protein. By clicking onto an isotope distribution graph the corresponding peaks are displayed in the main window.
The command Window > Tasks shows a list of very specific tasks.