Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

Yafeng Zhu, Lukas M. Orre, Henrik J. Johansson, Mikael Huss, Jorrit Boekel, Mattias Vesterlund, Alejandro Fernandez-Woodbridge, Rui M. M. Branca () and Janne Lehtiö ()
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Yafeng Zhu: Karolinska Institutet
Lukas M. Orre: Karolinska Institutet
Henrik J. Johansson: Karolinska Institutet
Mikael Huss: Stockholm University
Jorrit Boekel: Karolinska Institutet
Mattias Vesterlund: Karolinska Institutet
Alejandro Fernandez-Woodbridge: Karolinska Institutet
Rui M. M. Branca: Karolinska Institutet
Janne Lehtiö: Karolinska Institutet

Nature Communications, 2018, vol. 9, issue 1, 1-14

Abstract: Abstract Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3–10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific.

Date: 2018
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DOI: 10.1038/s41467-018-03311-y

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