Accurate Prediction of Protein Sequences for Proteogenomics Data Integration.

This book chapter discusses proteogenomics data integration and provides an overview into the different omics layer involved in defining the proteome of a living organism. Various aspects of genome variability affecting either the sequence or abundance level of proteins are discussed in this book chapter, such as the effect of single-nucleotide variants or larger genomic structural variants on the proteome. Next, various sequencing technologies are introduced and discussed from a proteogenomics data integration perspective such as those providing short- and long-read sequencing and listing their respective advantages and shortcomings for accurate protein variant prediction using genomic/transcriptomics sequencing data. Finally, the various bioinformatics tools used to process and analyze DNA/RNA sequencing data are discussed with the ultimate goal of obtaining accurately predicted sample-specific protein sequences that can be used as a drop-in replacement in existing approaches for peptide and protein identification using popular database search engines such as MSFragger, SearchGUI/PeptideShaker.