ReviewNature protocols2023
PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries.
Review in Nature protocols, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 32 citations in OpenAlex.
- Preclinical proof of concept for a personalized SNAP™-TIL (Specific Neo-Antigen Peptides-TIL) therapy platform.Oncoimmunology · 2026Article
- Reconstructing pathogen-specific antibody binding epitopes and age-dependent immune signatures from proteomic-scale peptide libraries.Science advances · 2026Article
- Empowering One Health with metagenomics.One health outlook · 2026Review
- Peptide Arrays as Tools for Unraveling Tumor Microenvironments and Drug Discovery in Oncology.Cells · 2026Review
- Addressing gaps in the diagnoses of genetic errors of immunity.Nature immunology · 2025Article
- Reconstructing pathogen-specific antibody binding epitopes and age-dependent immune signatures from proteomic-scale peptide libraries.medRxiv : the preprint server for health sciences · 2025Article
- Identification of Coccidioidomycosis Immunoreactive Peptides That Recall T-Cell Responses Indicating Past Exposure.The Journal of infectious diseases · 2025Article
- High-throughput multiplexed serology via the mass-spectrometric analysis of isotopically barcoded beads.Nature biomedical engineering · 2025Article
- Assessing the performance of TRX and DUF148 antigens for detection of prepatent Guinea worm (Frontiers in parasitology · 2025Article
- PepSeq as a highly multiplexed platform for melioidosis antigen discovery and vaccine development.Frontiers in immunology · 2025Article
- Direct Mapping of Polyclonal Epitopes in Serum by HDX-MS.Analytical chemistry · 2024Article
- Article
- Article
- Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error.PLoS computational biology · 2024Article
- Serum antibody screening using glycan arrays.Chemical Society reviews · 2024Review
- Recurrent SARS-CoV-2 mutations at Spike D796 evade antibodies from pre-Omicron convalescent and vaccinated subjects.Microbiology spectrum · 2024Article
- Quantitative assessment of multiple pathogen exposure and immune dynamics at scale.Microbiology spectrum · 2024Article
- Pathogen Discovery in the Post-COVID Era.Pathogens (Basel, Switzerland) · 2024Review
- PhIP-Seq: methods, applications and challenges.Frontiers in bioinformatics · 2024Review
- Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides.International journal of molecular sciences · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
18 authors at 3 institutions in 1 country.
Funding
Abstract
PepSeq is an in vitro platform for building and conducting highly multiplexed proteomic assays against customizable targets by using DNA-barcoded peptides. Starting with a pool of DNA oligonucleotides encoding peptides of interest, this protocol outlines a fully in vitro and massively parallel procedure for synthesizing the encoded peptides and covalently linking each to a corresponding cDNA tag. The resulting libraries of peptide/DNA conjugates can be used for highly multiplexed assays that leverage high-throughput sequencing to profile the binding or enzymatic specificities of proteins of interest. Here, we describe the implementation of PepSeq for fast and cost-effective epitope-level analysis of antibody reactivity across hundreds of thousands of peptides from <1 µl of serum or plasma input. This protocol includes the design of the DNA oligonucleotide library, synthesis of DNA-barcoded peptide constructs, binding of constructs to sample, preparation for sequencing and data analysis. Implemented in this way, PepSeq can be used for a number of applications, including fine-scale mapping of antibody epitopes and determining a subject's pathogen exposure history. The protocol is divided into two main sections: (i) design and synthesis of DNA-barcoded peptide libraries and (ii) use of libraries for highly multiplexed serology. Once oligonucleotide templates are in hand, library synthesis takes 1-2 weeks and can provide enough material for hundreds to thousands of assays. Serological assays can be conducted in 96-well plates and generate sequencing data within a further ~4 d. A suite of software tools, including the PepSIRF package, are made available to facilitate the design of PepSeq libraries and analysis of assay data.
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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.