MassIVE MSV000096529

Partial Public PXD058291

Proteomic analyses of bacterial growth using fungal biomass or fungal cell wall polysaccharides

Description

This study was a proteomic and secretomic survey of the Gram-negative saprophytic bacterium Cellvibio japonicus during growth using fungal polysaccharides or authentic fungal biomass as a sole nutrient source. The purified polysaccharides were beta-glucan (derived from yeast) and alpha chitin (derived from shrimp shells). The authentic fungal biomass came from Saccharomyces cerevisiae and Aspergillus nidulans. The proteome and secretome samples were taken during mid-exponential growth in biological triplicate. Bacterial cells were homogenized via probe sonication and reduced and alkylated followed by trypsin digestion using a suspension trap (S-trap). Supernatants were reduced and alkylated and followed by trypsin digestion via MStern Blotting. An SPQC was made by combining equal volumes of each sample for both sample types. After lyophilization and reconstitution, 2 ul of cell digests and 15 ul of supernatant digests were loaded onto Evotips. Quantitative LC/MS/MS was performed using an Evosep One LC coupled to a Thermo Orbitrap Astral via a Nanospray Flex ionization source. Samples were block randomized and interspersed with the SPQC replicates. The Evosep used a 60 sample-per-day method with a Pepsep 8 cm x 150 um column (1.5 um particle size) with a PepSep Sprayer and stainless steel (30 um) emitter. The MS analysis used a 240,000 resolution precursor ion (MS1) scan from 380-980 m/z, AGC target of 500% and maximum injection time (IT) of 50 ms, collected every 0.6 s in centroid mode. MS/MS was performed using a DIA method with default charge state = 3, precursor mass range of 380-980, 10 m/z isolation windows, AGC target of 500% and maximum IT of 20 ms, and a NCE of 28. An RF lens of 40% was used for MS1 and DIA scans. Raw MS data was converted to .htrms format using HTRMS converter and processed in Spectronaut 19 (Biognosys). A spectral library was built using direct-DIA searches of all DIA analyses using a Cellvibrio japonicus database, downloaded from Uniprot on 10/29/2024 and appended contaminant sequences using FragPipeSearch settings included N-terminal trypsin/P specificity up to 2 missed cleavages; peptide length from 7-52 amino acids with the following modifications: acetyl (N-term) and carbamidomethyl(Cys). For DIA analysis, default extraction, calibration, identification, and protein inference settings were used. [doi:10.25345/C57P8TR5T] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Cellvibrio japonicus ; Carbohydrate Active Enzyme ; Polysaccharide Degradation ; Beta-glucan ; Chitin ; Fungal Biomass ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order)
Jeffrey G. Gardner, University of Maryland - Baltimore County (UMBC), USA
Submitting User: mviolette
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Experimental Design
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Identification Results
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Quantification Results
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.