ArticleNature methods2012
De novo derivation of proteomes from transcriptomes for transcript and protein identification.
Article in Nature methods, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
80 citing papers in PubMed.
- Multi-platform omics analysis of Nipah virus infection reveals viral glycoprotein modulation of mitochondria.Cell reports · 2025Article
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- Adenovirus E1B-55K controls SUMO-dependent degradation of antiviral cellular restriction factors.Journal of virology · 2023Article
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- Overview and considerations in bottom-up proteomics.The Analyst · 2023Review
- The AMP deaminase of the mollusk Helix pomatia is an unexpected member of the adenosine deaminase-related growth factor (ADGF) family.PloS one · 2023Article
- Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis.Genome research · 2023Article
- Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts.PLoS pathogens · 2022Article
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva.Parasites & vectors · 2022Article
- Proteotranscriptomics - A facilitator in omics research.Computational and structural biotechnology journal · 2022Review
- Coelenterazine sulfotransferase from Renilla muelleri.PloS one · 2022Article
- Discovery of a small protein-encoding cis-regulatory overlapping gene of the tumor suppressor gene Scribble in humans.Communications biology · 2021Article
- Adenovirus Remodeling of the Host Proteome and Host Factors Associated with Viral Genomes.mSystems · 2021Article
- MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses.Database : the journal of biological databases and curation · 2021Article
- Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing.Nature microbiology · 2020Article
- Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein.Genome medicine · 2020Article
- Article
- Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution.Communications biology · 2020Article
- Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain.Life science alliance · 2020Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.