Abstract

Proteogenomics are defined as the combination between proteomics and genomics techniques, which allows the construction of databases for specific populations in order to improve the identification of peptides not found in canonical sequences with conventional nLC-MS/MS. We use a protegenomics approach to investigate the proteome of human saliva samples (n=6) from healthy young woman at fertile age. Transcriptome libraries were obtained through TruSeqHT kit and sequenced in house using NextSeq 500 platform (Illumina). The results were filtered by quality, adapter cutting, filter by species and assembly. The result was translated with GeneMark-HMM software and was used as reference for subsequent proteomics analysis. Proteins were extracted utilizing a standard protocol. The obtained mix of peptides were quantified by IR and solved by nanoHPLC (nanoElute) Mass Spectometry using our TimsTOFpro instrument (Bruker). Protein identification was performed using the PEAKS studio X with the transcriptomic database generated above. The results were annotated against Uniprot/Swisprot database (560,292 entries). Functional annotation was performed through KAAS, GO and Reactome. Overall 23.754 human transcript were obtained representing an average of 11,2% of total mRNA in samples. These sequences were used as customized database and combined with the MS results, which produced a total of 36,243Peptide-Spectrum Matches. A total of 2,513 peptides and 668 proteins were identified by this combined approach. Functional annotation identified proteins know to be constitutive from saliva, sugar metabolism and dental apparatus. Proteogenomics appear to be a promissory approach for the research of potential biomarkers of human health and disease in Chilean women.