Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification

To increase the number of virus species that can be detected we developed a shotgun proteomics based approach, which was applied to viral samples, after which the identified peptides were searched for in a database equipped with proteomic data of 46 viruses, known to be infectious to humans, using a web application (‘proteome2virus.com’). To validate proteome2virus application (proteome2virus.com) data of cultured and clinical samples was generated. The method has been successfully tested against cultured viruses and 8 clinical fecales samples of 10 different viral species from 7 different virus families, including SARS-CoV-2, Betacoronavirus OC43, human coronavirus 229E, human orthopneumovirus (RSV A and RSV B), human metapneumovirus, Influenza A (H1N1 and H3N2), mamastrovirus 1, Norwalk virus, Rotavirus A and human mastadenovirus F, representing 7 different virus families. The samples were prepared with two different sample preparation methods and were measured on two different mass spectrometers. Results demonstrated that the developed data analysis pipeline is applicable to different MS data sets generated on 2 different instruments and that it this approach identifies a high variety of clinically relevant viral species. This emphasizes the potential and feasibility for the diagnosis of a wide range of viruses in clinical samples with a single shotgun proteomics analysis.