This tutorial will go through the basics of loading a database and setting up a project. PEAKS is able to read publicly available and custom made database as long as they are in the fasta format. By organizing files in projects, it helps to keep work organized, and within PEAKS they remain stable and even allow the processing of extremely large files…think files hundreds of gigabytes large.

Load a Database

Start by setting up a database. PEAKS provides us with a sample FASTA database called “SampleDB.fasta” in our PEAKS program folder. Click on the configuration toolbar icon or select “Configuration” from the “Tools” menu. Select “Database” from the left hand side of the window. Under “Database Details”, select SwissProt, give the database a name, and specify a path to the database. You do not need to change any of the other information listed. Click the “Add/Update” button and then click “OK”.

Create a Project

The next step is to create a project. This will be a rather simple project, as it will only contain one sample; however the same process will be used for projects with multiple samples and files. Click on the “Create new project” button or select “New Project” from the “File” menu.
Enter a name for your project. By default the first sample will be named “Sample 1”. Click the “Add data files” button to add a data file for sample 1. Select the “OrbiSample.mzxml” file from your PEAKS program folder (for example “C:\PEAKSStudio5.3\Data”) and click “Open”. Leave the instrument vendor as “All Instruments” and select “FT-trap” from the “Instrument Type” drop-down list. Click “OK”.
You should now see it in the “Project View” panel to the left.
Use the ‘+’ and ‘-’ boxes to expand and collapse the project in order to access the data file in the “Project View”. Make sure that you select this data file when choosing data to be analyzed. PEAKS reads and tracks information about the experiment and data for use in the analysis and for future reference. Once the data file has loaded, the fraction icon will turn solid. Click on the “Properties” tab in the bottom left hand corner.
In the “Main Processing Window” the information that is displayed by default pertains to the precursor scan. To the left of the window is the “Total Ion Chromatogram” (TIC). The graph in the upper right corner displays a survey scan with its corresponding tandem scans below. Click on the MS/MS tab to see the graphs that were generated from the tandem scan.

Perform Data Refinement

1) Click the Data Refine toolbar icon or select “Data Refine” from the “Tools” menu.
2) Enter the settings, correct precursor charge states, between 1 and 4. Here we will use a quality filter to remove data with a quality value lower than 0.65. As all of the data in this data set is of good quality, we will not end up removing any data using this filter. Preprocess the data, yes. Click OK. After running data refine, there will be new information listed in the “Properties” file.

Click here to continue on to the next tutorial, dedicated to de novo sequencing.