De novo derivation of proteomes from transcriptomes for transcript and protein identification
Open accessAbstract
Identification of proteins by tandem mass spectrometry requires a reference protein database, but these are only available for model species. Here we demonstrate that, for a non-model species, the sequencing of expressed mRNA can generate a protein database for mass spectrometry-based identification. This combination of high-throughput sequencing and protein identification technologies allows detection of genes and proteins. We use human cells infected with human adenovirus as a complex and dynamic model to demonstrate the robustness of this approach. Our proteomics informed by transcriptomics (PIT) technique identifies >99% of over 3,700 distinct proteins identified using traditional analysis that relies on comprehensive human and adenovirus protein lists. We show that this approach can also be used to highlight genes and proteins undergoing dynamic changes in post-transcriptional protein stability.
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RNA sequencing can build sample-specific proteoform databases that capture genetic variation and splicing patterns, allowing the strategy to be extended to mammalian genomes.
“To extend the strategy to mammalian genomes, RNA sequencing can be used to construct sample-specific proteoform databases that capture the genetic variation and extent of splicing patterns in the sample (10, 11).”
From Proteoforms as the next proteomics currency (2018) · cites this paper as [11]
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- Authors
- Evans, V. C., Barker, G., Heesom, K. J., Fan, J., Bessant, C., & Matthews, D. A.
- Affiliations
- University of Bristol (GB)
- Cranfield University (GB)
- Corresponding author
- Matthews, David A
- Venue
- Nature Methods
- Published
- 2012-11-11
- Volume
- 9
- Issue
- 12
- Pages
- 1207-1211
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3581816
- OpenAlex
- W2052775071
- Cited by
- 166
- References
- 33
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 2 · 2023: 7 · 2022: 12 · 2021: 4 · 2020: 15 · 2019: 15 · 2018: 16 · 2017: 14 · 2016: 15 · 2015: 22 · 2014: 30 · 2013: 7
- FWCI
- 8.36
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Explore Bristol Research (submittedVersion)
- Funders
- Wellcome Trust (083604)
- Biotechnology and Biological Sciences Research Council (BB/I001131/1, BB/I00095X/1)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- non-model organisms, human cells
- MeSH terms
- Adenoviridae, Animals, Arginine, Carbon Isotopes, Chromatography, Liquid, Cricetulus, Cricetinae, HeLa Cells, Humans, Lysine, Nitrogen Isotopes, Nuclear Proteins, RNA, Messenger, Software, CHO Cells, RNA-Binding Proteins, Sequence Analysis, Protein, Proteome, Polymorphism, Single Nucleotide, Databases, Protein, Proteomics, Tandem Mass Spectrometry, Transcriptome
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