title: De novo identification and quantification of single amino-acid variants in human brain.
abstract: The detection of single amino-acid variants (SAVs) usually depends on single-nucleotide polymorphisms (SNPs) database. Here, we describe a novel method that discovers SAVs at proteome level independent of SNPs data. Using mass spectrometry-based de novo sequencing algorithm, peptide-candidates are identified and compared with theoretical protein database to generate SAVs under pairing strategy, which is followed by database re-searching to control false discovery rate. In human brain tissues, we can confidently identify known and novel protein variants with diverse origins. Combined with DNA/RNA sequencing, we verify SAVs derived from DNA mutations, RNA alternative splicing, and unknown post-transcriptional mechanisms. Furthermore, quantitative analysis in human brain tissues reveals several tissue-specific differential expressions of SAVs. This approach provides a novel access to high-throughput detection of protein variants, which may offer the potential for clinical biomarker discovery and mechanistic research.
authors.affiliation: Key Laboratory of Systems Biology, Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
authors.forename: Zhi-Duan
authors.initials: ZD
authors.lastname: Su
authors.affiliation: Key Laboratory of Systems Biology, Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
authors.forename: Quan-Hu
authors.initials: QH
authors.lastname: Sheng
authors.affiliation: Key Laboratory of Systems Biology, Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
authors.forename: Qing-Run
authors.initials: QR
authors.lastname: Li
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Chi
authors.affiliation: Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yan
authors.affiliation: Key Laboratory of Systems Biology, Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Fu
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Si-Min
authors.initials: SM
authors.lastname: He
authors.affiliation: Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Philipp
authors.initials: P
authors.lastname: Khaitovich
authors.affiliation: Key Laboratory of Systems Biology, Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China wujr@sibs.ac.cn zr@sibs.ac.cn.
authors.forename: Jia-Rui
authors.initials: JR
authors.lastname: Wu
authors.affiliation: Key Laboratory of Systems Biology, Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China wujr@sibs.ac.cn zr@sibs.ac.cn.
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
mesh_terms: D000595:Amino Acid Sequence; D001921:Brain / Q000378:metabolism*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D014176:Protein Biosynthesis; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
keywords: de novo; human brain tissues; proteomics; single amino-acid variants (SAVs)