MassIVE MSV000089106

Partial Public PXD032724

Nickel Binding- and Histidine-Rich Proteins of Helicobacter species

Description

The files in this archive examine six species within the genus Helicobacter to assay their histidine-rich proteins. They correspond to the manuscript "Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species" by Frederic Fischer, Egor Vorontsov, Evelyne Turlin, Christian Malosse, Camille Garcia, David L. Tabb, Julia Chamot-Rooke, Riccardo Percudani, Daniel Vinella and Hilde De Reuse. The sequence databases for the Helicobacter species are based on reference or complete UniProt proteomes in FASTA format, supplemented with reannotations of Hpn and Hpn2 protein products. The full list of RAW files, including their attribution to individual species and the type of experiment they represent, can be found in RAWs-Readme. We have included QuaMeter IDFree metrics to include basic statistics such as length of LC gradient, the number of MS/MS scans, etc. [doi:10.25345/C5ZK55Q89] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: gastric ; IMAC ; nickel ; reannotation

Contact

Principal Investigators:
(in alphabetical order)
Hilde De Reuse, Institut Pasteur, France
Submitting User: dtabb73

Publications

Fischer F, Vorontsov E, Turlin E, Malosse C, Garcia C, Tabb DL, Chamot-Rooke J, Percudani R, Vinella D, De Reuse H.
Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species.
Metallomics.

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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.

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.

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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.

"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.