Quick Start Guide

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 Kojak configuration file in this directory.


Step 2: Edit your configuration file

A. Open Kojak.conf in a text editor.

B. Change MS_data_file to your data file.

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

C. Name your output_file and percolator_file.

output_file = C:\Data\MyProject\DataFile1-results.txt
percolator_file = C:\Data\MyProject\DataFile1-perc

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 Kojak.conf and exit the text editor.

Step 3: Run Kojak

A. Open a command line prompt.

B. Navigate to the Kojak folder.

cd C:\Kojak 

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

Kojak.exe C:\Data\MyProject\Kojak.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-percolator.txt > DataFile1-validated.txt 

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