De novo identification and quantification of single amino-acid variants in human brain
peer-reviewed · Journal of Molecular Cell Biology · 2014
| Date | 2014-10-01 |
| Type | peer-reviewed |
| Venue | Journal of Molecular Cell Biology |
| Publisher | Oxford University Press (OUP) |
| Contribution | downstream-application |
| DOI | 10.1093/jmcb/mju031 |
| Citations (OpenAlex) | 9 |
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.
Methods and tools
- De novo SAV discovery: Discovers single amino-acid variants without SNP databases by pairing de novo sequencing candidates against theoretical proteins, then re-searching to control FDR; applied to human brain tissue.