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- W2247147930 abstract "ABSTRACT Gene annotation and gene model construction has so far been based mainly on analysis of DNA sequence and transcription of DNA into RNA. This approach has of course proven its validity in annotating most of the human genome, although it has several limitations. We present here a paradigm shift as we open up the possibility of using mass spectrometry data in an unbiased genome-wide search for protein coding DNA sequence in the human genome. Using high resolution isoelectric focusing on peptide level (HiRIEF) couple to LC-MS/MS analysis we can facilitate matching of the peptides to entire human ORF space with high accuracy. Here we demonstrate an effective workflow for genome wide proteomegenomics in humans by describing 71 new human gene models detected in human cell line A431. The method facilitates also an in-depth analysis on complex proteomes, a requirement for efficient proteogenomics experiments. The novel protein-coding gene models are supported by high confidence peptides, mRNAseq data from same samples, evolutionary conservation analysis and in several cases ortholog protein expression in other species. Here we demonstrate new human novel short open reading frames expressed on protein level, novel splice forms, altered transcription start sites and pseudogenes that translates a protein. To demonstrate the use of the method we profiled three other human cell lines (A549, MCF7 and PC3) demonstrating that several of the new gene models could be detected in these cell lines as well." @default.
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- W2247147930 date "2012-06-01" @default.
- W2247147930 modified "2023-10-03" @default.
- W2247147930 title "P3.04 Genome Wide Proteomics Using Peptide High Resolution Isoelectric Focusing Hirief-Ms Allows Detection New Human Gene Models" @default.
- W2247147930 doi "https://doi.org/10.1016/s0923-7534(20)31357-0" @default.
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