MassIVE MSV000090315

Partial Public

SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus

Subscribe Comment Convert Spectra Add Reanalysis

Description

Protein samples were measured using the LC-MS/MS platform containing reversed-phase nano liquid chromatography (nano Acquity M-class UPLC) (Waters Corporation, Massachusetts, USA), which was coupled to nanospray ionization tandem mass spectrometry with traveling wave ion mobility using high-definition data-independent (HD-MSE) acquisition and enabled with hybrid quadrupole orthogonal acceleration time of flight mass spectrometer (Synapt G2Si, Waters Corporation). The peptide mixture was separated on ACQUITY UPLC M-Class HSS T3 1.8 um, 75 um x 200 mm column (Waters Corporation) using a mixture of Buffers A (0.1% v/v Acetic acid in water) and B (0.1% v/v acetic acid in acetonitrile) through a linear concentration gradient of Buffer B in 170 min, with a flow rate of 300 nl/min from 5-26% (v/v). The eluents were sprayed at a voltage of 1.85-1.90 kV using PicoTip emitters (Waters Corporation), and other source parameters were set (sampling cone = 40V, source offset = 0 V, source temperature = 80C, gas flows, cone gas = 50 l/h, nano gas flow = 0.4 bar, purge gas = unchanged, IMS = optimized for wave velocity with a start velocity of 870 m/s to end at 564 m/s that corresponds to the separation of GluFib fragments in the drift time range of 0-200 bins). The data was acquired using the MassLynx software program version V4.1 (Waters Corporation) that automatically switches between MS and MS/MS (HDMSE) scans in resolution mode at 20000 with 1 second (sec) scan time and the scan range of 50-2000 m/z. Calibration was done by injecting GluFib at an interval of 1 min. The acquired data were analyzed for protein identifications against the Uniprot fasta database of B. cereus ATCC14579 strain that contained 5240 sequences via the PLGS v3.3 program (Water Corporation). Spectra were processed using low and high-energy thresholds of 135, 20 counts, and lock mass calibration 785.8456 m/z for GluFib. The workflow search parameters were set as: (protease = trypsin, one missed cleavage, carbamidomethyl for cysteine as fixed, variable modifier = oxidation of methionine). The protein was quantified when 1) the top 3 peptides had no modifications; 2) pass one match had peptide fragment one; and 3) ranked the first three highest peptides. The PLGS independent identification output was imported to ISOQuant 1.8 (Distler et al., 2014) for sample analyses. [doi:10.25345/C5Z892K4R] [dataset license: CC0 1.0 Universal (CC0 1.0)] [doi:10.25345/C5PR7MZ7B] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Bacillus cereus ; sigB ; heat stress

Contact

Principal Investigators:
(in alphabetical order) 		Prof. Dr. Uwe Voelker, University Medicine Greifswald, Germany
Submitting User: stemicha

Publications

Yeak KYC, Tempelaars M, Wu JL, Westerveld W, Reder A, Michalik S, Dhople VM, Völker U, Pané-Farré J, Wells-Bennik MHJ, Abee T.
SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus.
BMC Microbiol. 2023 Feb 10;23(1):37. Epub 2023 Feb 10.

Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
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.

"N/A" means no results of this type were submitted.
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.