BBSRC iCase - Development of an automated, high-resolution analysis pipeline for bacterial peptidoglycan structural analyses

Lead Research Organisation: University of Sheffield
Department Name: Molecular Biology and Biotechnology

Abstract

This project will build on our preliminary work to develop a novel pipeline for PG structure analysis that combines high mass accuracy LC-MS/MS and automated analysis of fragmentation spectra.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011151/1 01/10/2015 30/09/2023
2058718 Studentship BB/M011151/1 01/10/2017 30/11/2021 Ankur Patel
 
Title Automated data analysis of tandem mass spectrometry of non linear molecules (branched or crosslinked) 
Description Optimised pipeline for data acquisition using liquid chromatography and tandem mass spectrometry coupled to data analysis software to automate data analysis. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact One manuscript in favourable review in Nature Microbiology & one paper in Cell. 
 
Description Analysis of peptidoglycan bound proteins in gram negative pathogens 
Organisation National Institute of Allergy and Infectious Diseases (NIAID)
Department Rocky Mountain Laboratories
Country United States 
Sector Public 
PI Contribution Using the peptidoglycan (PG) analysis pipeline designed during this PhD project, we showed that several gram negative pathogens produce beta barrel proteins that are covalently anchored to PG. These proteins have been shown to be essential for cell envelope integrity in the model organism Coxiella burnetii.
Collaborator Contribution Our partners provided biological samples that we analysed.
Impact One manuscript in favourable revision in Nature microbiology.
Start Year 2018
 
Description Characterisation of L-D Transpeptidase activity from a novel type 6 secretion system effector 
Organisation Universidade de São Paulo
Country Brazil 
Sector Academic/University 
PI Contribution Data analysis of peptidoglycan treated with a novel T6SS effector
Collaborator Contribution Provided biological material
Impact Paper in review in EMBO
Start Year 2019
 
Description Data analysis on provided peptidoglycan samples. 
Organisation University of Montana
Country United States 
Sector Academic/University 
PI Contribution Performed data analysis on peptidoglycan samples sent by collaborators confirming a symbiotic relationship between a fly species and two bacteria in its gut.
Collaborator Contribution Provides biological samples.
Impact Paper in Cell. DOI: 10.1016/J.CELL.2019.08.054
Start Year 2019
 
Title Automated analysis of tandem mass spectrometry data fron nojn linear molecules 
Description Software enables the analysis of non linear molecules (branched or crosslinked) such as peptidoglycan, antibodies and cyclic molecules without sample processing to generate short linear peptides. This is achieved by representing the molecule in silico as a graph comprising nodes that represent the building blocks of the molecule and edges describing the bonds between nodes. 
Type Of Technology Software 
Year Produced 2019 
Impact Software is still in development but has shown the ability to analyse peptidoglycan monomers and dimers. 
 
Title Automated identification of muropeptides from MS1 data 
Description Automated identification of muropeptides within MS1 data using a simple initial search library and optional 'smart' in silico modification generation to minimise false positives and facilitate removal of search space bias due to time requirements in manual analysis. 
Type Of Technology Webtool/Application 
Year Produced 2021 
Open Source License? Yes  
Impact Software currently in final form is using python code. Jupyter notebook interface near completion. Publication of software and its application in journal currently in work.