Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using MS-Based Targeted Proteomics

• Published in: Viruses Vol. 11; no. 6; p. 536
• Main Authors: Lechner, Johanna, Hartkopf, Felix, Hiort, Pauline, Nitsche, Andreas, Grossegesse, Marica, Doellinger, Joerg, Renard, Bernhard Y, Muth, Thilo
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 08-06-2019; MDPI
• Subjects: Candidates; Computer applications; Computer programs; data analysis; Databases, Protein; Design; Experiments; Humans; Mass Spectrometry; Mass spectroscopy; Open source software; parallel reaction monitoring; Pathogens; peptide selection; Peptide synthesis; Peptides; Peptides - analysis; Proteins; Proteome; Proteomes; Proteomics; Proteomics - methods; Public health; Reproducibility; Reproducibility of Results; Scientific imaging; Software; targeted proteomics; Taxonomy; Viral infections; virus diagnostics; Virus Diseases - diagnosis; virus proteomics; Viruses; Workflow; data analysis; peptide selection; parallel reaction monitoring; targeted proteomics; virus diagnostics; mass spectrometry; virus proteomics
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v11060536

Emerging virus diseases present a global threat to public health. To detect viral pathogens in time-critical scenarios, accurate and fast diagnostic assays are required. Such assays can now be established using mass spectrometry-based targeted proteomics, by which viral proteins can be rapidly detected from complex samples down to the strain-level with high sensitivity and reproducibility. Developing such targeted assays involves tedious steps of peptide candidate selection, peptide synthesis, and assay optimization. Peptide selection requires extensive preprocessing by comparing candidate peptides against a large search space of background proteins. Here we present Purple (Picking unique relevant peptides for viral experiments), a software tool for selecting target-specific peptide candidates directly from given proteome sequence data. It comes with an intuitive graphical user interface, various parameter options and a threshold-based filtering strategy for homologous sequences. Purple enables peptide candidate selection across various taxonomic levels and filtering against backgrounds of varying complexity. Its functionality is demonstrated using data from different virus species and strains. Our software enables to build taxon-specific targeted assays and paves the way to time-efficient and robust viral diagnostics using targeted proteomics.