Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.
Yafeng ZhuLukas M OrreHenrik J JohanssonMikael HussJorrit BoekelMattias VesterlundAlejandro Fernandez-WoodbridgeRui M M BrancaJanne LehtiöPublished in: Nature communications (2018)
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.
Keyphrases
- amino acid
- ms ms
- endothelial cells
- small molecule
- high throughput
- high resolution
- genome wide
- electronic health record
- induced apoptosis
- gene expression
- induced pluripotent stem cells
- protein protein
- liquid chromatography tandem mass spectrometry
- pluripotent stem cells
- deep learning
- copy number
- dna methylation
- big data
- binding protein
- tandem mass spectrometry
- signaling pathway
- rna seq
- single cell
- simultaneous determination