Quick Start Guide

This quick start guide just gives the barest example of how one might quickly analyze their spectra using Magnum. Your actual pipeline requirements might differ and it is recommended that you read and follow the complete instructions provided elsewhere on this website before using Magnum.

Step 1: Set up a data project folder

A. Create a folder or directory on your computer hard drive.


B. Copy or link your data to this directory.


C. Create a copy of the Magnum configuration file in this directory.


Step 2: Edit your configuration file

A. Open Magnum.conf in a text editor.

B. Change MS_data_file to your data file.

MS_data_file = C:\Data\MyProject\DataFile1.mzML 

C. Specify any additional output formats.

export_percolator = 1
export_pepXML = 1

D. Change database to the amino acid sequence database you want to use.

database = C:\FASTA\MyDatabase.fasta 

E. Set other parameters as necessary. Parameters and descriptions can be found on the Parameters page.

F. Save Magnum.conf and exit the text editor.

Step 3: Run Magnum

A. Open a command line prompt.

B. Navigate to the Magnum folder.

cd C:\Magnum 

C. Execute the Magnum application with the path and name of your configuration file.

Magnum.exe C:\Data\MyProject\Magnum.conf 

Step 4: Validate and Summarize Results

A. Navigate to your data folder

cd C:\Data\MyProject 

B. Execute the Percolator application

C:\Percolator\Percolator.exe DataFile1.perc.txt > DataFile1-validated.txt 

C. View your DataFile1-validated.txt results file in any text editor or spreadsheet application (such as Excel).