Evidence map›Paper›PMID 25167056›Full record

ArticleNature protocols2014

Bio-orthogonal labeling as a tool to visualize and identify newly synthesized proteins in Caenorhabditis elegans.

Milena Ullrich, Vanessa Liang, Yee Lian Chew, Samuel Banister, Xiaomin Song, Thiri Zaw, Hong Lam, Slavica Berber, Michael Kassiou, Hannah R Nicholas and 1 more

Erratum issuedAbstract read
PubMed Publisher
In one paragraph

Article in Nature protocols, 2014. 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 26 papers.

0numbers the graph read from it
0cells of the map it votes in
26citing papers in PubMed
1.5field-weighted citation impact, top 21% 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

26 citing papers in PubMed, 45 citations in OpenAlex.

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  7. MACSPI enables tissue-selective proteomic and interactomic analyses in multicellular organisms.Proceedings of the National Academy of Sciences of the United States of America · 2024
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  19. Revealing nascent proteomics in signaling pathways and cell differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  20. Article
4 · The record

Corrections and comments

  • Erratum issued
5 · Who and what money

Authors and funding

11 authors at 2 institutions in 2 countries.

Milena Ullrich1] Brain and Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia. [2] Institute for Integrative Neuroanatomy, Charité, Universitätsmedizin Berlin, Berlin, Germany.
Vanessa LiangBrain and Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia.
Yee Lian ChewSchool of Molecular Bioscience, University of Sydney, Camperdown, New South Wales, Australia.
Samuel BanisterSchool of Chemistry, University of Sydney, Camperdown, New South Wales, Australia.
Xiaomin SongAustralian Proteome Analysis Facility, Macquarie University, Sydney, New South Wales, Australia.
Thiri ZawAustralian Proteome Analysis Facility, Macquarie University, Sydney, New South Wales, Australia.
Hong LamSchool of Molecular Bioscience, University of Sydney, Camperdown, New South Wales, Australia.
Slavica BerberSchool of Molecular Bioscience, University of Sydney, Camperdown, New South Wales, Australia.
Michael Kassiou1] School of Chemistry, University of Sydney, Camperdown, New South Wales, Australia. [2] Faculty of Health Sciences, Macquarie University, Sydney, New South Wales, Australia.
Hannah R Nicholas1] School of Molecular Bioscience, University of Sydney, Camperdown, New South Wales, Australia. [2].
Jürgen Götz1] Brain and Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia. [2] Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, Brisbane, Queensland, Australia. [3].
University of Sydney · AUMacquarie University · AU

Funding

Enhancing and expanding the CGC Strain CollectionP40OD010440 · OD · UNIVERSITY OF MINNESOTA · PI Ann E. Rougvie · 2012 to 2026
$7.5M
NIH HHS P40 OD010440
6 · The paper itself

Abstract

In this protocol we describe the incorporation of bio-orthogonal amino acids as a versatile method for visualizing and identifying de novo-synthesized proteins in the roundworm Caenorhabditis elegans. This protocol contains directions on implementing three complementary types of analysis: 'click chemistry' followed by western blotting, click chemistry followed by immunofluorescence, and isobaric tags for relative and absolute quantification (iTRAQ) quantitative mass spectrometry. The detailed instructions provided herein enable researchers to investigate the de novo proteome, an analysis that is complicated by the fact that protein molecules are chemically identical to each other, regardless of the timing of their synthesis. Our protocol circumvents this limitation by identifying de novo-synthesized proteins via the incorporation of the chemically modifiable azidohomoalanine instead of the natural amino acid methionine in the nascent protein, followed by facilitating the visualization of the resulting labeled proteins in situ. It will therefore be an ideal tool for studying de novo protein synthesis in physiological and pathological processes including learning and memory. The protocol requires 10 d for worm growth, liquid culture and synchronization; 1-2 d for bio-orthogonal labeling; and, with regard to analysis, 3-4 d for western blotting, 5-6 d for immunofluorescence or ~3 weeks for mass spectrometry.

Indexed as

AlanineAmino AcidsAnimalsBlotting, WesternCaenorhabditis elegans ProteinsChemistry Techniques, AnalyticalClick ChemistryFluorescent Antibody TechniqueMass SpectrometryStaining and LabelingAlanineAmino AcidsazidohomoalanineCaenorhabditis elegans Proteins

Identifiers

PMID25167056
OpenAlexW2033319851

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.