Commands:
File > Import > Mass Data...
File > Export > Spetrum Description...
Spectra and Chromatograms
Arcadiate imports individual spectra as [m/z (tab) intensity] lists in ASCII format. Chromatographic data is imported in mzData, mzXML or mzML format. Mass spectrometric chromatographic data can be very complex. Currently Arcadiate supports only the most simple format: MS spectra mixed with tandem MS spectra. Both types should be homogeneous. This means all MS spectra and all tandem MS spectra should be each a group of spectra with the same mass spectrometric characteristic (see below). A good programme for converting mass spectrometric data to xml format is MSConvert in the Proteowizard Package.
Several files can be selected using the command File > Import > Mass Data....
Arcadiate attempts to automatically detect the file type and displays the Import Window. The Import Window contains a table of all the files to be imported with several parameters describing the data. These parameter should correctly reflect the data characteristics.
Centroided data can only be imported when a spectrum description file is available for this type of data. A spectrum description is a central element in how Arcadiate stores and displays mass spectrometric data. When profile data is imported two spectrum descriptions are generated automatically, one for the MS and a second for the tandem MS data. A spectrum description describes the m/z-axis value spacing, the typical peak shape and how this peak shape changes with m/z. A spectrum description file can be exported using the command File > Export > Spetrum Description.... Take care that the profile data contains tandem MS spectra so that the two spectrum descriptions for MS and tandem MS data are generated and exported. The exported file has to be used to import centroided mass spectra. The centroided data is treated and displayed in the same way as the profile data the spectrum description was generated from.