Evidence map›Paper›PMID 38941022›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Label-Free Quantitative Proteomics of Oral Microbial Communities.

Marwan Mansoor Ali Mohammed, Jack-Ansgar Bruun, Veronika Kuchařová Pettersen

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

3 authors.

Marwan Mansoor Ali MohammedDepartment of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates. mmmohammed@sharjah.ac.ae.
Jack-Ansgar BruunProteomics and Metabolomics Core Facility (PRiME), Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway.
Veronika Kuchařová PettersenResearch Group for Host-Microbe Interaction, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The oral cavity is a habitat for different microorganisms, of which bacteria are best described. Studying different bacterial taxa and their proteins is crucial to understanding their interactions with the host and other microbes. Also, for bacteria with virulence potential, identifying novel antigenic proteins is essential to finding candidates for the development of vaccines.Here, a workflow for gel-free and label-free protein analysis of oral bacterial species grown in vitro as a biofilm and a planktonic culture is described. Details on cultivation, protein extraction and digestion, peptide cleanup, LC-MS/MS run parameters, and subsequent bioinformatics analysis are included. Challenging steps in the workflow, such as growing different types of bacteria and selecting a suitable protein database, are also discussed. This protocol provides a valuable guide for metaproteomic experiments using multi-species models of oral bacteria.

Indexed as

BacteriaBacterial ProteinsMouthProteomicsTandem Mass SpectrometryBiofilmsChromatography, LiquidComputational BiologyHumansMicrobiotaProteomeWorkflowBacterial ProteinsProteomeFusobacterium nucleatumLabel-free quantitative metaproteomicsMulti-species modelOral biofilmOral microbiologyOral pathogenic bacteriaPorphyromonas gingivalis

Identifiers

PMID38941022

What OpenQuestion holds

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Registered trials

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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.