PXD058291

PXD058291 is an original dataset announced via ProteomeXchange.

Title	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.
HostingRepository	MassIVE
AnnounceDate	2024-11-26
AnnouncementXML	Submission_2024-11-26_09:09:49.995.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marlene Violette
SpeciesList	scientific name: Cellvibrio japonicus; NCBI TaxID: 155077;
ModificationList	Acetyl; Carbamidomethyl
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-26 08:03:38	ID requested
⏵ 1	2024-11-26 09:09:50	announced

no publication

submitter keyword: Cellvibrio japonicus, Carbohydrate Active Enzyme, Polysaccharide Degradation, Beta-glucan, Chitin, Fungal Biomass, DatasetType:Proteomics

Jeffrey G. Gardner
contact affiliation	University of Maryland - Baltimore County (UMBC)
contact email	jgardner@umbc.edu
lab head
Marlene Violette
contact affiliation	Duke University
contact email	marlene.violette@duke.edu
dataset submitter

MassIVE dataset URI

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v07/MSV000096529/