Automated Extraction of Proteotypic Peptides by Shotgun Proteomic Experiments: A New Computational Tool and Two Actual Cases

The rapid development of mass spectrometry-based proteomic technologies has allowed the quantification and validation of protein biomarkers toward detection of signature molecules, called proteotypic peptides. To facilitate their extraction from experimental protein and peptide lists, we present here a friendly computational tool called Experimental Proteotypic Peptides Investigator (EPPI). In this study, it was used for extracting proteotypic peptides from two collections of experimental data obtained by MudPIT analysis of adipose and gut human tissue. In particular, EPPI allows the selection of peptides presenting higher occurrence, evaluates their uniqueness by molecular weight and amino-acid sequence, and takes into consideration combinations of multiple proteotypic peptides (proteotypic peptide sets) for evaluating their capacity to target a single protein. In fact, in combination with high-resolution MS instruments, it could be a starting point for targeting proteins by following only precursor ions in full MS scan mode. The software is available under the permissive Apache 2.0 open-source license, and the code can be accessed from https://github.com/ITB-ProtMet/eppi.git.