Summary of Study ST002159

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001372. The data can be accessed directly via it's Project DOI: 10.21228/M8CH8H This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002159
Study TitleChemotaxonomic patterns in intracellular metabolites of marine microbial plankton
Study SummaryTargeted and untargeted metabolomes were generated for a variety of marine microbial taxa including eukaryotic phytoplankton, cyanobacteria, archaea, and heterotrophic bacteria. Microbial metabolism generates small organic molecules that reflect both the biochemical and physiological diversity as well as the taxonomic specificity of biological processes. These small molecules serve as the conduit for taxon-specific signaling and exchange. We used liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to taxonomically categorize metabolites that include small molecules in central and secondary metabolism across 42 taxa representing numerically dominant and metabolically important lineages of microbial autotrophs and heterotrophs.
Institute
University of Washington
DepartmentOceanography
LaboratoryIngalls
Last NameDurham
First NameBryndan
Address2033 Mowry Rd., CGRCRm 404
Emailb.durham@ufl.edu
Phone3522946312
Submit Date2021-12-10
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2022-05-16
Release Version1
Bryndan Durham Bryndan Durham
https://dx.doi.org/10.21228/M8CH8H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001372
Project DOI:doi: 10.21228/M8CH8H
Project Title:Marine microbial culture metabolomics
Project Summary:Targeted and untargeted metabolomes were generated for a variety of marine microbial taxa including eukaryotic phytoplankton, cyanobacteria, archaea, and heterotrophic bacteria.
Institute:University of Washington
Department:Oceanography
Laboratory:Ingalls
Last Name:Durham
First Name:Bryndan
Address:2033 Mowry Rd CGRC 415
Email:b.durham@ufl.edu
Phone:3522946312
Funding Source:NSF and Simons Foundation
Publications:Durham et al., Frontiers in Marine Science

Subject:

Subject ID:SU002245
Subject Type:Cultured cells
Subject Species:Marine Plankton

Factors:

Subject type: Cultured cells; Subject species: Marine Plankton (Factor headings shown in green)

mb_sample_id local_sample_id Replicate
SA206996180130_Blk_MediaBlk_11
SA206997180130_Smp_Exp_11
SA206998180130_Smp_Exp_22
SA206999180130_Smp_Exp_33
SA207000180227_Smp_116-1_AA
SA207001170821_Blk_FilterBlk_As9601A
SA207002170821_Smp_Nat_AA
SA207003170821_Blk_FilterBlk_NatA
SA207004161114_Blk_MediaBlk_CA
SA207005180227_Smp_P3_AA
SA207006161114_Smp_8102_AA
SA207007180227_Blk_MediaBlk_LInoSiA
SA207008161114_Blk_MediaBlk_AA
SA207009170821_Blk_FilterBlk_OA
SA207010170821_Smp_1545_AA
SA207011170821_Blk_FilterBlk_21A
SA207012180227_Smp_3430_AA
SA207013161116_Smp_SA60_AA
SA207014180227_Blk_MediaBlk_RAC5A
SA207015170821_Smp_1314P_AA
SA207016170821_Smp_As9601_AA
SA207017161107_Smp_2090_AA
SA207018161107_Blk_MediaBlk_AA
SA207019161107_Smp_SA30_AA
SA207020180227_Smp_Ca_AA
SA207021161116_Smp_SA16_AA
SA207022161116_Blk_MediaBlk_BA
SA207023170117_Smp_SA48_AA
SA207024161116_Smp_SA42_AA
SA207025170117_Smp_SA53_AA
SA207026170117_Blk_MediaBlk_AA
SA207027170117_Smp_SA11_AA
SA207028170117_Smp_DSS3_AA
SA207029170213_Smp_SA55_A_rerunA
SA207030161116_Smp_SA59_AA
SA207031170117_Smp_SA36_AA
SA207032180227_Smp_Cs_AA
SA207033170213_Smp_SA7_A_rerunA
SA207034180227_Smp_Cr_AA
SA207035161107_Smp_SA33_AA
SA207036170117_Smp_Och_AA
SA207037170821_Smp_Tp10_AA
SA207038170821_Blk_FilterBlk_1314PA
SA207039161107_Blk_MediaBlk_DiatomCA
SA207040161107_Smp_Tp_AA
SA207041170821_Blk_FilterBlk_Tp10A
SA207042170213_Smp_Np_A_rerunA
SA207043161107_Blk_MediaBlk_DiatomAA
SA207044170213_Smp_Pcx_AA
SA207045161107_Blk_MediaBlk_DiatomBA
SA207046170821_Smp_Tp35_AA
SA207047170213_Smp_Pt_CA
SA207048161107_Smp_371_AA
SA207049170213_Blk_MediaBlk_Pc55xA
SA207050161107_Smp_To_AA
SA207051161107_Blk_MediaBlk_DiatomZA
SA207052170821_Smp_Tp28_AA
SA207053170821_Smp_1771_AA
SA207054170821_Smp_449_AA
SA207055161107_Blk_MediaBlk_DiatomYBCA
SA207056170821_Blk_FilterBlk_49A
SA207057170821_Blk_FilterBlk_NA
SA207058170821_Smp_1314_AA
SA207059170821_Blk_FilterBlk_71A
SA207060161107_Smp_Cy_AA
SA207061170821_Smp_2021_AA
SA207062161107_Smp_SA30_BB
SA207063170213_Smp_SA7_B_rerunB
SA207064170213_Smp_SA55_B_rerunB
SA207065170117_Smp_SA44_BB
SA207066170117_Smp_SA48_BB
SA207067170213_Blk_MediaBlk_BB
SA207068180227_Smp_Cr_BB
SA207069170821_Blk_FilterBlk_Tp28B
SA207070170117_Smp_DSS3_BB
SA207071161107_Smp_371_BB
SA207072180227_Smp_Ca_BB
SA207073170213_Smp_Np_C_rerunB
SA207074161107_Smp_SA33_BB
SA207075170117_Smp_SA11_BB
SA207076161107_Smp_Cy_BB
SA207077161116_Smp_SA16_BB
SA207078170117_Smp_Och_BB
SA207079161116_Smp_SA60_BB
SA207080170821_Smp_1314P_BB
SA207081170821_Smp_1314_BB
SA207082161107_Smp_SA42_BB
SA207083170821_Smp_As9601_BB
SA207084170821_Smp_1771_BB
SA207085161107_Smp_2090_BB
SA207086161114_Smp_8501_BB
SA207087170821_Smp_1545_BB
SA207088170821_Smp_Tp10_BB
SA207089170821_Smp_449_BB
SA207090180227_Smp_3430_BB
SA207091180227_Smp_116-1_BB
SA207092170821_Smp_Tp28_BB
SA207093170117_Smp_SA36_BB
SA207094170821_Smp_Tp35_BB
SA207095170821_Smp_2021_BB
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 157

Collection:

Collection ID:CO002238
Collection Summary:Cultured marine plankton cells grown to mid-to-late exponential phase were filtered onto 0.2-micron durapore filters and extracted for metabolites according to extraction protocol.
Sample Type:Plankton cells

Treatment:

Treatment ID:TR002257
Treatment Summary:Marine plankton were cultured according to standard protocols.

Sample Preparation:

Sampleprep ID:SP002251
Sampleprep Summary:Marine plankton cells were extracted using the described protocols. Each sample was extracted using a modified Bligh-Dyer extraction. Briefly, filters were cut up and split between two bead beating tubes containing a mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal standards were added along with 750 µL of cold aqueous solved (50:50 methanol:water) and 750 µL of cold organic solvent (dichloromethane). The samples were shaken on a FastPrep-24 Homogenizer for 30 seconds and chilled in a -20 ∞C freezer repeatedly for three cycles of beadbeating and a total of 30 minutes of chilling. The organic and aqueous layers were separated by spinning samples in a microcentrifuge at 5,000 rpm for 90 seconds at 4 ∞C. The aqueous layer was removed to a new glass centrifuge tube. The remaining organic fraction was rinsed three more times with additions of 750 µL of 50:50 methanol:water. All aqueous rinses were combined for each sample and dried down under N2 gas. The remaining organic layer was transferred into a clean glass centrifuge tube and the remaining bead beating tube was rinsed two more times with cold organic solvent. The combined organic rinses were centrifuged, transferred to a new tube, and dried under N2 gas. Dried aqueous fractions were re-dissolved in 380 µL of water. Dried organic fractions were re-dissolved in 380 µL of 1:1 water:acetonitrile. 20 µL of isotope-labeled injection standards in water were added to both fractions. Blank filters were extracted alongside samples as methodological blanks.
Sampleprep Protocol Filename:SP_Ingalls_extraction_protocol.pdf

Combined analysis:

Analysis ID AN003535 AN003536 AN003537 AN003538
Analysis type MS MS MS MS
Chromatography type HILIC HILIC HILIC Reversed phase
Chromatography system Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class
Column SeQuant ZIC- pHILIC (150 x 2.1mm, 5um) SeQuant ZIC- pHILIC (150 x 2.1mm, 5um) SeQuant ZIC- pHILIC (150 x 2.1mm, 5um) Waters Acquity UPLC HSS Cyano (100 x 2.1 mm, 1.8um)
MS Type ESI ESI ESI ESI
MS instrument type Triple quadrupole Orbitrap Orbitrap Orbitrap
MS instrument name Waters Xevo-TQ-S Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode UNSPECIFIED POSITIVE NEGATIVE POSITIVE
Units presence (1), absence (0), or background level (NA) presence (1), absence (0), or background level (NA) presence (1), absence (0), or background level (NA) presence (1), absence (0), or background level (NA)

Chromatography:

Chromatography ID:CH002611
Chromatography Summary:For HILIC chromatography, a SeQuant ZIC-pHILIC column (5 µm particle size, 2.1 mm x 150 mm, from Millipore) was used with 10 mM ammonium carbonate in 85:15 acetonitrile to water (Solvent A) and 10 mM ammonium carbonate in 60:40 water to acetonitrile (Solvent B) at a flow rate of 0.15 mL/min.
Methods Filename:CH_Ingalls_LC_protocol.pdf
Instrument Name:Waters Acquity I-Class
Column Name:SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)
Chromatography Type:HILIC
  
Chromatography ID:CH002612
Chromatography Summary:For reversed phase (RP) chromatography, a Waters Acquity UPLC HSS Cyano column (1.8 µm particle size, 2.1 mm x 100 mm) equipped with a Waters Acquity UPLC HSS Cyano guard column (1.8 µm particle size, 2.1 mm x 5 mm) was used with 0.1% formic acid in water (Solvent A) and 0.1% formic acid in acetonitrile (Solvent B) at a flow rate of 0.4 mL/ min.
Methods Filename:CH_Ingalls_LC_protocol.pdf
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity UPLC HSS Cyano (100 x 2.1 mm, 1.8um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003293
Analysis ID:AN003535
Instrument Name:Waters Xevo-TQ-S
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:MS acquisition according to attached protocol.
Ion Mode:UNSPECIFIED
Analysis Protocol File:Ingalls_Metabolomics_MS_Parameters_2015.txt
  
MS ID:MS003294
Analysis ID:AN003536
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS acquisition according to attached protocol.
Ion Mode:POSITIVE
Analysis Protocol File:Ingalls_Metabolomics_MS_Parameters_2015.txt
  
MS ID:MS003295
Analysis ID:AN003537
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS acquisition according to attached protocol.
Ion Mode:NEGATIVE
Analysis Protocol File:Ingalls_Metabolomics_MS_Parameters_2015.txt
  
MS ID:MS003296
Analysis ID:AN003538
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS acquisition according to attached protocol.
Ion Mode:POSITIVE
Analysis Protocol File:Ingalls_Metabolomics_MS_Parameters_2015.txt
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