MassIVE MSV000099245

Partial Public

Genomic analysis uncovers diverse Salmonella T6SS effectors and lipid-targeting antibacterial toxins

Subscribe Comment Convert Spectra Reanalyze Spectra Add Reanalysis

Description

E. coli MG1655 containing the plasmids pBRA SP-Tox-Act1WT or SP-Tox-Act1C151A were cultured in LB and resuspended in AB supplemented with 0.2% L-arabinose to induce Tox-Act1 expression. Cell pellets were resuspended and the lipid-containing phase was extracted. Lipid extracts were analyzed using ultra-high-performance liquid chromatography (UHPLC Nexera, Shimadzu) coupled with an ESI-Q-TOF mass. MS and MS/MS data acquisition was performed using Analyst 1.7.1 software (Sciex). Mass spectrometry data was inspected using PeakView 2.0 software (Sciex), and lipid molecular species were manually identified with the help of an in-house manufactured Excel-based macro. Lipid species were quantified using MultiQuant software (Sciex), where the precursor ions areas were normalized by the internal standards for each class. [doi:10.25345/C5N29PK9R] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: lipidomics ; polymorphic toxin ; DatasetType:Other (lipidomics)

Contact

Principal Investigators:
(in alphabetical order) 		Ethel Bayer-Santos, University of Texas, USA
Gianlucca G Nicastro, National Library of Medicine, USA
Robson Francisco de Souza, University of Sao Paulo, Brazil
Submitting User: rfsouza
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.