The Proteome Discoverer application offers numerous options for exporting data and search results into file formats. You can export the following:
- Spectra from the search results to these file formats: (You can export spectra even though they do not identify any peptides.)
- Mascot Generic Format (MGF): Places the exported spectra into MGF files that contain a list of precursor ions, their fragments, and the masses of the fragments.
- MZDATA: Places the exported spectra into MZDATA files, which are common data format files developed by the Human Proteome Organization (HUPO) for proteomics mass spectrometry data. These files are in version 1.05 format. They are exported with XML indentation enabled so that the different XML tags are broken into multiple lines instead of merged into one line.
- MZML: Places the exported spectra into MZML files, which are a combination of .mzData and .mzXML formats developed by the Human Proteome Organization Standard Initiative (HUPO-PSI) and the Seattle Proteome Center at the Institute for Systems Biology (ISB). The Proteome Discoverer application supports version 1.1.0 of the MZML format. - Annotated spectra into a ZIP file that includes an HTML page with peptide information and links to spectrum images
- Search results to tab-delimited TXT files
- Search results to XML files
- Protein references and sequences in the search results to a FASTA file
- Mass lists to the Xcalibur data system
- Graphs to the Clipboard to save in EMF, PNG, GIF, JPG, TIFF, or BMP files
- Sample information from a study into a study definition text or Excel file