MassIVE MSV000085508

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GNPS - Undiagnosed Disease Network Study Results, Plasma lipidomics and metabolomics

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Description

The deposited data were collected from 148 patients and 133 family members accepted into the Undiagnosed Diseases Network (https://undiagnosed.hms.harvard.edu/). The NIH Common Fund Undiagnosed Diseases Network (UDN) seeks to provide diagnoses for individuals with undiagnosed disease. Here, we report and provide the mass spectrometry-based metabolomics (GC-MS) and lipidomics (LC-MS/MS) analyses of blood plasma from 148 patients and 133 family members. We have deposited mass spectrometry-based metabolomics and lipidomics files including instrument files, normalized data processed files to allow for statistical analysis, and metabolomics and lipidomics results for each patient and associated relatives. In addition, as part of the mass spectrometry data made available, we have included mass spectrometry analyses and results from a reference population of individuals with no known metabolic diseases. UDN patients suffer from undiagnosed diseases and thus are typically represented as a sample size of one; therefore, understanding normal variation within a proband's condition needs to be measured against of dataset of normal individuals, which is included here. [doi:10.25345/C5P11F] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: metabolomics ; lipidomics ; rare disease ; undiagnosed diseases ; plasma

Contact

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

Publications

Kyle JE, Stratton KG, Zink EM, Kim YM, Bloodsworth KJ, Monroe ME, Undiagnosed Diseases Network, Waters KM, Webb-Robertson BM, Koeller DM, Metz TO.
A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases.
Sci Data. 2021 Apr 21;8(1):114. Epub 2021 Apr 21.

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Identification Results
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Quantification Results
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Species

Instrument

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GNPS content goes here (MSV000085508 [task=b1a702e030304dad878d58d8aaedf210])
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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.