Evidence map›Paper›PMID 33811468›Full record

ArticleProteomics2021

Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies.

Chen Li, Jerico Revote, Sri H Ramarathinam, Shan Zou Chung, Nathan P Croft, Katherine E Scull, Ziyi Huang, Rochelle Ayala, Asolina Braun, Nicole A Mifsud and 3 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Proteomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
0.6field-weighted citation impact, top 34% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 9 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 2 institutions in 2 countries.

Chen LiDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID https://orcid.org/0000-0002-1847-754X
Jerico RevoteMonash Bioinformatics Platform, Monash University, Melbourne, Victoria, Australia.
Sri H RamarathinamDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID https://orcid.org/0000-0002-2787-1282
Shan Zou ChungDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Nathan P CroftDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID https://orcid.org/0000-0002-2128-5127
Katherine E ScullDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Ziyi HuangDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Rochelle AyalaDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Asolina BraunDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Nicole A MifsudDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Patricia T IllingDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Pouya FaridiDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID https://orcid.org/0000-0002-2712-3356
Anthony W PurcellDepartment of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID https://orcid.org/0000-0003-0532-8331
Discovery Institute · USMelbourne Bioinformatics · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

SARS-CoV-2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS-CoV-2, identifying potential T cell epitopes derived from the SARS-CoV-2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS-CoV-2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user-friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide-HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.

Indexed as

COVID-19SARS-CoV-2HumansPeptidesProteomicsTandem Mass SpectrometryPeptidesCOVID19databaseLC-MSSARS-CoV-2synthetic peptidestandem mass spectrometry

Identifiers

PMID33811468
PMCPMC8250278
OpenAlexW3141551441

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.