A list of clinically significant genera/species (with at least two peptides) was used to generate a protein FASTA database within the Galaxy workflow. ![]() The detected peptides identified were subjected to Unipept 4.3 analysis to detect taxonomic information about microorganisms present in the sample. Peter Thuy-Boun from Wolan Lab at the Scripps Institute searched the twenty RAW files (five negative and positive samples along with a technical replicate each) using COMPIL 2.0 against a comprehensive 113 million protein sequence database. The mass spectrometry (MS) data was made available via ProteomeXchange (PXD020394) so as to facilitate the use of MS-based approaches for COVID-19 diagnosis.We were interested in detecting the presence of microorganisms apart from the SARS-CoV2 virus in the clinical samples. Tryptic peptides obtained from five COVID-19 positive and five COVID-19 negative samples were analysed by LC-MS/MS using a Q-Exactive Plus mass spectrometer. Rivera et al (opens new window) from Institut Pasteur de Montevideo and Universidad de la República (Montevideo, Uruguay) performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis.
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