MassIVE MSV000085713

Partial Public

GNPS - MetFish: A Metabolomics Platform for Studying Microbial Communities in Chemically Extreme Environments

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

Here we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exo-metabolomics analysis in sample matrices containing up to 2 molar total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and can be integrated into either targeted or untargeted analysis pipelines. MetFish was successfully applied in targeted and untargeted exo-metabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exo-metabolome during community succession; in situ in a native prairie soil, whose exo-metabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exo-metabolome over time in the well. [doi:10.25345/C53Q93] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: metabolomics ; high-salt samples ; microbial communities

Contact

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

Publications

Xu C, Couvillion SP, Sontag RL, Isern NG, Maezato Y, Lindemann SR, Roy Chowdhury T, Zhao R, Morton BR, Chu RK, Moore RJ, Jansson JK, Bailey VL, Mouser PJ, Romine MF, Fredrickson JF, Metz TO.
MetFish: a Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments.
mSystems. 2021 Jun 29;6(3):e0105820. Epub 2021 May 26.

Chengdong Xu, Sneha P. Couvillion, Ryan L. Sontag, Nancy G. Isern, Yukari Maezato, Stephen R. Lindemann, Taniya Roy Chowdhury, Rui Zhao, Beau R. Morton, Ronald J. Moore, Janet K. Jansson, Vanessa L. Bailey, Paula J. Mouser, Margaret F. Romine, James F. Fredrickson, Thomas O. Metz.
MetFish: A Metabolomics Platform for Studying Microbial Communities in Chemically Extreme Environments.
doi: https://doi.org/10.1101/518647.

Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

GNPS content goes here (MSV000085713 [task=d870a2f46c7b4965993778e456b36b2d])
Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

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.