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Detection of lipopeptides produced by strains of the P. syringae complex by MALDI-ToF

ABSTRACT: This project aimed at detecting and identifying the various lipopeptides produced by a collection of 724 strains belonging to the Pseudomonas syringae complex. Analyses were performed on whole-cells after growth on solid media at 25 degrees celsius for 72 hours.

INSTRUMENT(S): Bruker Autoflex Speed TOF/TOF

ORGANISM(S): Pseudomonas Syringae (ncbitaxon:317)

SUBMITTER: BRICOUT Alexandre

PROVIDER: MSV000087867 | MassIVE | Thu Jul 22 12:06:00 BST 2021

REPOSITORIES: MassIVE

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Fragmentation of lipopeptides produced by strains of the P. syringae complex by MALDI-MS-MS and LC-MS-MS

Project description:This project aimed at detecting and identifying the various lipopeptides produced by a collection of 724 strains belonging to the Pseudomonas syringae complex. Analyses were performed on whole-cells after growth on solid media at 25 degrees Celsius for 72 hours.

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Transcriptional profiling of Mms21 deleted (mms21Δ/Δ) mutant Candida albicans strains

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Identification of Bacillus strains by MALDI TOF MS using geometric approach.

Project description:Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to the Bacillus pumilus group. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species, Bacillus pumilus and Bacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available at http://www.bionet.nsc.ru/mbl/database/database.html.

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Rapid Identification of Escherichia coli Colistin-Resistant Strains by MALDI-TOF Mass Spectrometry.

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Project description:Transcriptome sequencing of Riemerella anatipestifer CH-1 under 37 degrees Celsius/42 degrees Celsius

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Top-down proteomic identification of plasmid and host proteins produced by pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry.

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The expression profiles of log-phase and stationary-phase cells of Shigella flexneri grown at 30 degrees and 37 degrees Celsius

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Project description:BACKGROUND: New strategies for high-throughput sequencing are constantly appearing, leading to a great increase in the number of completely sequenced genomes. Unfortunately, computational genome annotation is out of step with this progress. Thus, the accurate annotation of these genomes has become a bottleneck of knowledge acquisition. RESULTS: We exploited a proteogenomic approach to improve conventional genome annotation by integrating proteomic data with genomic information. Using Shigella flexneri 2a as a model, we identified total 823 proteins, including 187 hypothetical proteins. Among them, three annotated ORFs were extended upstream through comprehensive analysis against an in-house N-terminal extension database. Two genes, which could not be translated to their full length because of stop codon 'mutations' induced by genome sequencing errors, were revised and annotated as fully functional genes. Above all, seven new ORFs were discovered, which were not predicted in S. flexneri 2a str.301 by any other annotation approaches. The transcripts of four novel ORFs were confirmed by RT-PCR assay. Additionally, most of these novel ORFs were overlapping genes, some even nested within the coding region of other known genes. CONCLUSIONS: Our findings demonstrate that current Shigella genome annotation methods are not perfect and need to be improved. Apart from the validation of predicted genes at the protein level, the additional features of proteogenomic tools include revision of annotation errors and discovery of novel ORFs. The complementary dataset could provide more targets for those interested in Shigella to perform functional studies.

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