MassIVE MSV000090217

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Vibrio cholerae secDF1 whole cell proteomics

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Description

Whole cell pellets of Vibrio cholerae strains as described in Sit et al, 2022 (https://www.biorxiv.org/content/10.1101/2022.02.04.479082v1) Proteomics performed by the Thermo Center for Multiplexed Proteomics at Harvard Medical School using a standard fractionated total proteomics workflow. Each RAW file corresponds to one analyzed fraction out of twelve. Mapping of samples to tags is listed in the Supplementary File attached to this submission. BS001: WT V. cholerae (four replicates) BS553: delta secDF1 V. cholerae (three replicates). BS558, BS280, and BS338 correspond to strains analyzed in the same run but not presented in the manuscript. [doi:10.25345/C5HD7NX3C] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Vibrio cholerae cholera

Contact

Principal Investigators:
(in alphabetical order) 		Matthew Waldor, Brigham and Women's Hospital, USA
Submitting User: sitb

Publications

Sit B, Srisuknimit V, Bueno E, Zingl FG, Hullahalli K, Cava F, Waldor MK.
Undecaprenyl phosphate translocases confer conditional microbial fitness.
Nature. 2023 Jan;613(7945):721-728. Epub 2022 Nov 30.

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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.

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

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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.

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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.

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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.

"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.

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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.