ArticlePloS one2012
A highly scalable peptide-based assay system for proteomics.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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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
16 citing papers in PubMed, 23 citations in OpenAlex.
- mRNA Display for Identifying Peptide Substrates of Enzymes.Biochemistry · 2026Review
- Deep learning guided design of protease substrates.Nature communications · 2026Article
- Identification of Coccidioidomycosis Immunoreactive Peptides That Recall T-Cell Responses Indicating Past Exposure.The Journal of infectious diseases · 2025Article
- PepSeq as a highly multiplexed platform for melioidosis antigen discovery and vaccine development.Frontiers in immunology · 2025Article
- PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries.Nature protocols · 2023Review
- Analysis of intracellular tyrosine phosphorylation in circulating neutrophils as a rapid assay for theFrontiers in pharmacology · 2023Article
- Comprehensive analysis of transglutaminase substrate preference by cDNA display coupled with next-generation sequencing and bioinformatics.Scientific reports · 2022Article
- COVID-19 vaccination elicits an evolving, cross-reactive antibody response to epitopes conserved with endemic coronavirus spike proteins.Cell reports · 2022Article
- COVID-19 vaccination recruits and matures cross-reactive antibodies to conserved epitopes in endemic coronavirus Spike proteins.medRxiv : the preprint server for health sciences · 2022Article
- Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses.Cell reports. Medicine · 2021Article
- Assays for tyrosine phosphorylation in human cells.Methods in enzymology · 2019Article
- Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics.Molecular & cellular proteomics : MCP · 2016Article
- High-Throughput Multiplexed Peptide-Centric Profiling Illustrates Both Substrate Cleavage Redundancy and Specificity in the MMP Family.Chemistry & biology · 2015Article
- Structural and functional diversity of metalloproteinases encoded by the Bacteroides fragilis pathogenicity island.The FEBS journal · 2014Article
- Substrate cleavage profiling suggests a distinct function of Bacteroides fragilis metalloproteinases (fragilysin and metalloproteinase II) at the microbiome-inflammation-cancer interface.The Journal of biological chemistry · 2013Article
- High-resolution analysis and functional mapping of cleavage sites and substrate proteins of furin in the human proteome.PloS one · 2013Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
We report a scalable and cost-effective technology for generating and screening high-complexity customizable peptide sets. The peptides are made as peptide-cDNA fusions by in vitro transcription/translation from pools of DNA templates generated by microarray-based synthesis. This approach enables large custom sets of peptides to be designed in silico, manufactured cost-effectively in parallel, and assayed efficiently in a multiplexed fashion. The utility of our peptide-cDNA fusion pools was demonstrated in two activity-based assays designed to discover protease and kinase substrates. In the protease assay, cleaved peptide substrates were separated from uncleaved and identified by digital sequencing of their cognate cDNAs. We screened the 3,011 amino acid HCV proteome for susceptibility to cleavage by the HCV NS3/4A protease and identified all 3 known trans cleavage sites with high specificity. In the kinase assay, peptide substrates phosphorylated by tyrosine kinases were captured and identified by sequencing of their cDNAs. We screened a pool of 3,243 peptides against Abl kinase and showed that phosphorylation events detected were specific and consistent with the known substrate preferences of Abl kinase. Our approach is scalable and adaptable to other protein-based assays.
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What OpenQuestion holds
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.