Commands:
File > View > Save Table as Text...

File > Import > Arcadiate xml...
File > Import > Arcadiate txt...
File > Import > Mass Data...
File > Import > Database Searches...
File > Import > IonGroups...
File > Import > Molecular Markers...
File > Import > Proteins...

File > Export > Arcadiate xml...
File > Export > Arcadiate txt...
File > Export > Spectrum Description...
File > Export > Protein Quantifications...
,File > Export > Spectrum...
File > Export > Precursor...
File > Export > Ions...
File > Export > Peptides...
File > Export > Proteins...
File > Export > Molecular Markers...
File > Export > Chromatogram as mzML...
File > Export > Database Search Result as xml...
File > Export > Fragment Spectra for Mascot Search...

Edit > Cut


Arcadiate supports two generic export and import file formats that allow the exchange of database objects like chromatograms or database search results between two different users: the arcXML and the arcTxt format (File > Export > Arcadiate xml..., File > Export > Arcadiate txt... , File > Import > Arcadiate xml... , File > Import > Arcadiate txt... ). The arcTxt format can serve as a template how to build a file from external information to import it into Arcadiate - like a Molecular Marker Group.

arcXML and arcTxt files do not capture relationships between objects - like fragment spectra assignments to peptide sequences or quantifications of proteins. To export those various export commands had been implemented which most often export in tabular form (File > Export > Protein Quantifications..., File > Export > Ions..., File > Export > Peptides.., File > Export > Proteins..., File > Export > Molecular Markers...).

Some export commands follow public standards to support interactivity with other programmes (File > Export > Chromatogram as mzML..., File > Export > Database Search Result as xml..., File > Export > Fragment Spectra for Mascot Search, File > Export > Spectrum...).

The command File > View > Save Table as Text... represents a "best effort" to export a table as seen in Arcadiate in tabbed text format for import into spread sheet programmes.

With the help of a Spectrum Description file exported from a chromatogram that contains profile intact ion and fragment ion spectra centroided spectra can be imported (File > Export > Spectrum Description...). A Spectrum Description file captures the peak shape, the x-axis spacing and the resolution of mass spectra and describes therefore the mass spectrometer used. For some mass spectrometers such files can be downloaded from the Arcadiate Web Page.

Several import commands read in data from external sources. They are a starting point for using Arcadiate. Some use public standard format (File > Import > Mass Data... , File > Import > Database Searches... ), some simple tabular data (File > Import > Mass Data... for spectra, File > Import > IonGroups... ), others use more arbitrary tabular formats (File > Import > Molecular Markers... , File > Import > Proteins... ). These arbitrary formats reflect the problem to reflect tree-like data structures in tabular form. An xml data structure is the appropriate text format to reflect trees. The arcTxt format solves this problem systematically for simple trees and is the recommended import format for external data which is not xml.

Import of Mass Spectrometric Data
Import of spectra and chromatograms.

Import of Search Results
Import Mascot or MaxQuant Search Results to correlate it with your fragment spectra.

Import of Ion Groups
Import Ion Groups to quantify specific chromatographic ions.

Import of Molecular Markers
Import Molecular Markers to detect them in All Ion Fragmentation (MSE) chromatograms.

Import of Proteins
Import Proteins to quantify them in chromatograms.