MassIVE MSV000092668

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Rapid and in-depth proteomic profiling of small extracellular vesicles for ultralow samples

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Description

The form and function of extracellular vesicles (EV) is defined by their proteome. This knowledge is essential to describe and understand EVs, encompassing their marker proteins, capacity as a signalling platform, and utility as diagnostic tools and therapeutic targets. However, EV are low-abundant entities in the secreteome and biological samples, with disease-specific EV proteins often present in low abundance challenging their detection and quantification due to the inherent challenges in dynamic range using mass spectrometry-based strategies. Combined with lack of protein amplification mechanisms, their proteomic studies require upscaling cell cultures or larger volumes of biofluids. Here, we outline high-sensitivity sample preparation and finely tuned LC gradients for DIA to obtain precise and comprehensive proteome of EVs from ultra-low sample amounts (sub-nanogram). [doi:10.25345/C54M91M77] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Extracellular vesicles ; proteomics ; ultra-low proteomics ; subcellular ; high sensitivity ; mass spectrometry ; data-independent acquisition

Contact

Principal Investigators:
(in alphabetical order) 		David Greening, Baker Heart & Diabetes Institute, Australia
Submitting User: dwgree
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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.

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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.

"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.