Quick Start

To run MassSieve your system needs Java 8 or greater. Most OSX and Windows machines already have a Java environment. If yours does not, go to this website and download and install the Java Runtime Environment (JRE). You may also need to add the directory containing java.exe to your system path variable (availiable from Control Panels → System → Advanced → Environment Variables on windows).

After downloading and unzipping the latest stable binary, you can move the MassSieve folder to anywhere you like. There is no need to install it, it will run directly from the folder. You can just execute the MassSieve.jar file directly, but we recommend launching the program using the masssieve.bat on windows, or the masssieve.sh on OSX/Linux/Unix. This provides the java runtime with a larger memory environment allowing more than just trival datasets to be loaded.

Once the program is started, go to File → New Experiment to create a new experiment. You can add data to the experiment by using the File → Add Search Results... or the File → Batch Load Results... menu items. At this point in time, you can add Mascot .dat files and OMSSA .omx files. Any number of results files can be added to a single experiment. The data can be filtered by using the Tools → Change Filter menu item. Multiple experiments may be created and compared using the Tools → Compare Experiments menu item.

Additional hints

  • Protein sequence information can be loaded using File → Import Fasta...
  • Tables
    • Sorted by clicking on the column header.
    • Columns may be rearranged by dragging the column header.
    • Exported to CSV by Right-Clicking on the table.
  • Graphs
    • Panned by click-dragging the background.
    • Zoomed by using the mouse wheel.
    • Rearranged by dragging the elements.