OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.
Noé GuilloyMarie A BrunetSébastien LeblancJean-François JacquesMarie-Pierre HardyGrégory EhxJoël LanoixPierre ThibaultClaude PerreaultXavier RoucouPublished in: Journal of proteome research (2023)
Proteomic diversity in biological samples can be characterized by mass spectrometry (MS)-based proteomics using customized protein databases generated from sets of transcripts previously detected by RNA-seq. This diversity has only been increased by the recent discovery that many translated alternative open reading frames rest unannotated at unsuspected locations of mRNAs and ncRNAs. These novel protein products, termed alternative proteins, have been left out of all previous custom database generation tools. Consequently, genetic variations that impact alternative open reading frames and variant peptides from their translated proteins are not detectable with current computational workflows. To fill this gap, we present OpenCustomDB, a bioinformatics tool that uses sample-specific RNaseq data to identify genomic variants in canonical and alternative open reading frames, allowing for more than one coding region per transcript. In a test reanalysis of a cohort of 16 patients with acute myeloid leukemia, 5666 peptides from alternative proteins were detected, including 201 variant peptides. We also observed that a significant fraction of peptide-spectrum matches previously assigned to peptides from canonical proteins got better scores when reassigned to peptides from alternative proteins. Custom protein libraries that include sample-specific sequence variations of all possible open reading frames are promising contributions to the development of proteomics and precision medicine. The raw and processed proteomics data presented in this study can be found in PRIDE repository with accession number PXD029240.
Keyphrases
- mass spectrometry
- amino acid
- minimally invasive
- rna seq
- working memory
- acute myeloid leukemia
- big data
- protein protein
- single cell
- copy number
- binding protein
- electronic health record
- high resolution
- ms ms
- multiple sclerosis
- genome wide
- capillary electrophoresis
- high throughput
- acute lymphoblastic leukemia
- allogeneic hematopoietic stem cell transplantation