Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry
peer-reviewed · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · 2021
| Date | 2021-03-01 |
| Type | peer-reviewed |
| Venue | Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics |
| Publisher | Elsevier BV |
| Contribution | downstream-application |
| DOI | 10.1016/j.bbapap.2020.140594 |
| Citations (OpenAlex) | 5 |
Abstract
Eucalyptus species are widely used in the forestry industry, and a significant increase in the number of sequences available in database repositories has been observed for these species. In proteomics, a protein is identified by correlating the theoretical fragmentation spectrum derived from genomic/transcriptomic data against the experimental fragmentation mass spectrum acquired from large-scale analysis of protein mixtures. Proteogenomics is an alternative approach that can identify novel proteins encoded by regions previously considered as non-coding. This study aimed to confidently identify and confirm the existence of previously unknown protein-coding sequences in the Eucalyptus grandis genome. To this end, we used a modified spectral correlation strategy and a dedicated de novo peptide sequencing pipeline. Upon the strategy used here, we confidently identified 41 novel peptide forms and six peptides containing at least one single amino acid substitution. The most representative genomic class of novel peptides was identified as originating from alternative reading frames. In contrast, no clear single amino acid substitution pattern was identified. Validation of the identifications was carried out using a parallel reaction monitoring approach that provided further mass spectrometry support for the existence of the novel peptide sequences. Data are available via ProteomeXchange with identifier PXD022110.
Methods and tools
- Eucalyptus grandis novel protein-coding sequences: Proteogenomic search for unannotated proteins in Eucalyptus grandis using a dedicated de novo peptide sequencing pipeline (PEAKS plus PatternLab), confirming 41 novel peptide forms, mostly from alternative reading frames, by PRM.
Methods it uses
- PEAKS: Commercial DP-based de novo
- PepExplorer: Aligns de novo peptide sequences from several tools against a target-decoy database and uses a neural network to report homologous proteins at a controlled FDR.
Data deposited
- Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry — as deposited · PXD022110
Cites (4)
- Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications (2019) crossref
- Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics (2017) crossref
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012) crossref
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005) crossref