Abstract

In this tutorial, we will guide you through a bioinformatics workflow aimed at merging neoantigen databases with known human protein sequences, preparing the data for proteomics analysis using FragPipe. This workflow involves processing FASTA files, filtering for unique sequences, and validating the FASTA databases before using FragPipe to perform peptide identification and validation of neoantigens.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What are the key features and unique sequences in protein datasets that contribute to neoantigen discovery?
• How can we identify neoantigens from proteomic data?

Learning Objectives

• Understand the process of merging neoantigen databases with human protein sequences.
• Learn to use FragPipe for proteomics data analysis.
• Gain hands-on experience with bioinformatics tools such as FASTA file processing, database validation, and peptide identification.