title: Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs.
abstract: MS/MS has been used to improve genome annotation in various organisms. The classical approach is to construct comprehensive theoretical peptide database with six frame translation model from the whole ORF of a genome and search against this database with real MS/MS spectra. In this work we took a more focused approach, we constructed a database containing only peptides from the ab initio predicted genes from current human genome annotation, and all theoretical peptides from currently annotated lncRNAs, and searched such a database with MS/MS data from human Hela cell line. The purpose of this design is to find translation evidence for ab initio predicted genes and to rule out possible wrongly defined lncRNAs in a systematic proteogenomics effort. To validate proteogenomics results, we integrated RNA-Seq data analysis for the same Hela cell line which generated MS/MS data, and performed MRM experiment on self-cultured Hela cell line samples. Six peptides were found to support ab initio predicted genes with both RNA-Seq and MRM validations, while none was found to support a translated lncRNA. This workflow could be flexibly applied to other human samples and datasets to help further improve human gene annotation.
authors.affiliation: Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China; Key Laboratory of Systems Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Han
authors.initials: H
authors.lastname: Sun
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.forename: Meng
authors.initials: M
authors.lastname: Shi
authors.forename: Dandan
authors.initials: D
authors.lastname: Wang
authors.forename: Mingwei
authors.initials: M
authors.lastname: Liu
authors.forename: Daixi
authors.initials: D
authors.lastname: Li
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Yang
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.forename: Lu
authors.initials: L
authors.lastname: Xie
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D058977:Molecular Sequence Annotation; D017423:Sequence Analysis, RNA / Q000379:methods; D053719:Tandem Mass Spectrometry
keywords: Bioinformatics; Gene annotation; MRM; MS/MS; Proteogenomics; RNA-Seq