vPro-MS peptide spectral library for the identification of human-pathogenic viruses by untargeted proteomics

The viral proteomics workflow (vPro-MS) enables identification of human-pathogenic viruses from patient samples by untargeted proteomics. vPro-MS is based on an in-silico derived peptide library covering the human virome in UniProtKB (331 viruses, 20,386 genomes, 121,977 peptides). vPro-MS is intended to identify human-pathogenic viruses from DiaNN (https://github.com/vdemichev/DiaNN) outputs of either DIA or diaPASEF data. A scoring algorithm (vProID) assesses the confidence of virus identification and the results are finally summarized in a report table. 

The vPro Peptide Library folder contains 3 peptide FASTA files (Contaminants.fasta, Human.fasta, vPro.Virus.fasta), which were used to predict the spectral library (vPro-lib.predicted.speclib). Please note, that the additional commands “--cut” and “--duplicate-proteins” are needed to reprocess the prediction in DiaNN. This spectral library should be used to identify peptide sequences from samples of human origin using DiaNN. Furthermore, the folder contains the metadata file of the viral peptide sequences (vPro.Peptide.Library.txt) and a summary file of the virus taxonomy covered by the library (Taxonomy.Summary.txt). The metadata file is used by the vPro script to identify viruses from the DiaNN main report.