Magnum is run from a command line. For simplicity, only a single argument is required, the name of the configuration file. Details for setting your configuration file and the parameters contained within can be found from their respective links. The recommended way to operate Magnum is to store the data and configuration file in a convenient directory, navigate to it, then execute the Magnum application with the configuration file:
$ cd projects/data_set1 $ /usr/bin/magnum data_set1.conf
In the above example, you would substitute your own data directories, configuration file, and path to Magnum with the appropriate names and locations for your installation.
Microsoft Windows users may have difficulty finding their command line prompt. It can be quickly accessed from the Start Menu by typing "cmd" in the menu search box. Once open, it operates similarly to a Unix/Linux prompt (or perhaps more accurately, a DOS prompt).
The first statement you should see printed to the screen is the version, date, and source information for Magnum:
Magnum version 1.0.0, February 10 2021 Copyright Michael Hoopmann, Institute for Systems Biology
This information is important as Magnum is in continuous development and different versions may produce different results. It is recommended that you use the latest version of Magnum, but it may be helpful to also maintain legacy versions so that results may be replicated at a later date. Additionally, the version number is printed inside the Magnum results for your reference.
Analysis progress is reported during execution. The following stages are reported to the user:
- Database parsing - number of proteins and peptides to be searched.
- Spectra reading - number of spectra to be analyzed.
- Preprocessing - precursor mapping, etc.
- Spectral analysis
- E-value calculation and exporting results
The time at the completion of analysis is reported last and the command prompt is returned to the user.
After completion of the algorithm, several files will be exported to the storage device. Unless otherwise specified in the configuration file, exported files will be in the current working directory that you navigated to prior to starting Magnum.
All exported results are in text and/or XML format. The basic set of Magnum results is provided in the file set by the
An additional set of files containing the same results, but formatted for use with
Percolator, were exported with the base name
set from the