Evidence map›Paper›PMID 40133660›Full record

ArticleCommunications chemistry2025

A software tool and strategy for peptidoglycomics, the high-resolution analysis of bacterial peptidoglycans via LC-MS/MS.

Marcel G Alamán-Zárate, Brooks J Rady, Raphael Ledermann, Neil Shephard, Caroline A Evans, Mark J Dickman, Robert D Turner, Aline Rifflet, Ankur V Patel, Ivo Gomperts Boneca and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Activity Profiling of Mycobacterial L,D-Transpeptidases.bioRxiv : the preprint server for biology · 2026
    Article
  4. Review
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.

Marcel G Alamán-Zárate *Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK.ORCID http://orcid.org/0009-0007-0587-534X
Brooks J Rady *Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK.ORCID http://orcid.org/0000-0003-4763-4070
Raphael LedermannDepartment of Biology, University of Oxford, Oxford, UK.
Neil ShephardResearch Software Engineer team, University of Sheffield, Sheffield, UK.ORCID http://orcid.org/0000-0001-8301-6857
Caroline A EvansDepartment of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK.ORCID http://orcid.org/0000-0003-4356-9216
Mark J DickmanDepartment of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK.ORCID http://orcid.org/0000-0002-9236-0788
Robert D TurnerResearch Software Engineer team, University of Sheffield, Sheffield, UK.
Aline RiffletInstitut Pasteur, Université Paris Cité, INSERM U1306, CNRS UMR6047, Biology and genetics of the bacterial cell wall Unit, Paris, France.
Ankur V PatelMolecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK.
Ivo Gomperts BonecaInstitut Pasteur, Université Paris Cité, INSERM U1306, CNRS UMR6047, Biology and genetics of the bacterial cell wall Unit, Paris, France.ORCID http://orcid.org/0000-0001-8122-509X
Philip S PooleDepartment of Biology, University of Oxford, Oxford, UK.
Marshall BernProtein Metrics, 225 Franklin Street, Boston, USA.ORCID http://orcid.org/0000-0003-0342-9390
Stéphane MesnageMolecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK. s.mesnage@sheffield.ac.uk.ORCID http://orcid.org/0000-0003-1648-4890

Funding

RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/W013800/1
6 · The paper itself

Abstract

Peptidoglycan is an essential component of the bacterial cell envelope-a mesh-like macromolecule that protects the bacterium from osmotic stress and its internal turgor pressure. The composition and architecture of peptidoglycan is heterogeneous and changes as bacteria grow, divide, and respond to their environment. Though peptidoglycan has long been studied via LC-MS/MS, the analysis of this data remains challenging as peptidoglycan's unusual composition and branching can't be handled by proteomics software. Here we describe user-friendly open-source tools and a web interface for building peptidoglycan databases, performing MS searches, and predicting the MS/MS fragmentation of muropeptides. We then use Rhizobium leguminosarum to describe a step-by-step strategy for the high-resolution analysis of peptidoglycan. The unprecedented detail of R. leguminosarum's peptidoglycan composition (>250 muropeptides) reveals even the subtlest remodelling between growth conditions. These new and easier to use tools enable more systematic analyses of peptidoglycan dynamics.

Identifiers

PMID40133660
PMCPMC11937551

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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.