APEX TUTORIAL

The APEX module requires Thermo mass spectrometer files (.raw) and PatternLab for proteomics files (.sepr2) as input. It identifies peptides containing user-specified modifications and reporter ions.

HOW TO USE

1. Install and Open APEX

· Download the latest version of APEX from the link or access APEX in the 'Utils' tab on PatternLab for proteomics.

· Open the APEX.

2. Configure Analysis Parameters

2.1. Click "Browse" and select the folder containing .sepr2 files.

2.2. In "Params", choose the modification and reporter ion(s) to search. Use "AND" if all reporter ions are required, or "OR" if any reporter ion matches.

2.3. Set the "Ion Threshold (%)" - minimum reporter ion peak intensity relative to the highest MS/MS ion intensity.

2.4. Choose the "Fragment Error Tolerance" in Da or PPM.

2.5. In "Mode", select "Peptide" to report only modified peptides or "Protein" to include all identified peptides.

2.6. Click "GO" to start the analysis.

3. Result

3.1. The APEX results include:

· Total modified peptides - peptides with specified modifications (green bar).

· Modified peptides with reporter ions - subset with modifications and reporter ions (yellow bar).

4. Visualize the identified modified peptides/proteins in the SEPro module.

4.1. Load SEPro file

4.2. SEPro provides interactive graphs (e.g., annotated spectrum) and charts to explore the APEX results.