MassIVE MSV000091560

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TEDDY Proteomics Discovery Phase Study

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Description

In this set, we analyzed human plasma samples from The Environmental Determinants of Diabetes in the Young (TEDDY) Study. In total, 2,252 samples from 184 individuals were concatenated into 364 pooled samples from individuals that developed type 1 diabetes or islet autoimmunity and their matched controls. Samples were analyzed from the same individuals pre and post-autoimmunity onset paired against controls. Each pooled sample was depleted with MARS abundant protein depletion column (Agilent), digested with trypsin and labeled with 8-plex iTRAQ reagent. Samples were then multiplexed and fractionated into 24 fractions by high-pH reverse-phase chromatography (DOI: 10.1038/s41596-018-0006-9). Each fraction was analyzed by liquid chromatography tandem mass spectrometry. [doi:10.25345/C5V11VW3F] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: plasma ; type 1 diabetes ; biomarker ; abundant protein depletion ; 8-plex iTRAQ

Contact

Principal Investigators:
(in alphabetical order) 		Thomas Metz, Pacific Northwest National Laboratory, USA
Submitting User: teddystudy
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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.

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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.

"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.