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.

Study ID	ST002159
Study Title	Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton
Study Summary	Targeted 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
Department	Oceanography
Laboratory	Ingalls
Last Name	Durham
First Name	Bryndan
Address	2033 Mowry Rd., CGRCRm 404
Email	b.durham@ufl.edu
Phone	3522946312
Submit Date	2021-12-10
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2022-05-16
Release Version	1

Select appropriate tab below to view additional metadata details:

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
SA206996	180130_Blk_MediaBlk_1	1
SA206997	180130_Smp_Exp_1	1
SA206998	180130_Smp_Exp_2	2
SA206999	180130_Smp_Exp_3	3
SA207000	180227_Smp_116-1_A	A
SA207001	170821_Blk_FilterBlk_As9601	A
SA207002	170821_Smp_Nat_A	A
SA207003	170821_Blk_FilterBlk_Nat	A
SA207004	161114_Blk_MediaBlk_C	A
SA207005	180227_Smp_P3_A	A
SA207006	161114_Smp_8102_A	A
SA207007	180227_Blk_MediaBlk_LInoSi	A
SA207008	161114_Blk_MediaBlk_A	A
SA207009	170821_Blk_FilterBlk_O	A
SA207010	170821_Smp_1545_A	A
SA207011	170821_Blk_FilterBlk_21	A
SA207012	180227_Smp_3430_A	A
SA207013	161116_Smp_SA60_A	A
SA207014	180227_Blk_MediaBlk_RAC5	A
SA207015	170821_Smp_1314P_A	A
SA207016	170821_Smp_As9601_A	A
SA207017	161107_Smp_2090_A	A
SA207018	161107_Blk_MediaBlk_A	A
SA207019	161107_Smp_SA30_A	A
SA207020	180227_Smp_Ca_A	A
SA207021	161116_Smp_SA16_A	A
SA207022	161116_Blk_MediaBlk_B	A
SA207023	170117_Smp_SA48_A	A
SA207024	161116_Smp_SA42_A	A
SA207025	170117_Smp_SA53_A	A
SA207026	170117_Blk_MediaBlk_A	A
SA207027	170117_Smp_SA11_A	A
SA207028	170117_Smp_DSS3_A	A
SA207029	170213_Smp_SA55_A_rerun	A
SA207030	161116_Smp_SA59_A	A
SA207031	170117_Smp_SA36_A	A
SA207032	180227_Smp_Cs_A	A
SA207033	170213_Smp_SA7_A_rerun	A
SA207034	180227_Smp_Cr_A	A
SA207035	161107_Smp_SA33_A	A
SA207036	170117_Smp_Och_A	A
SA207037	170821_Smp_Tp10_A	A
SA207038	170821_Blk_FilterBlk_1314P	A
SA207039	161107_Blk_MediaBlk_DiatomC	A
SA207040	161107_Smp_Tp_A	A
SA207041	170821_Blk_FilterBlk_Tp10	A
SA207042	170213_Smp_Np_A_rerun	A
SA207043	161107_Blk_MediaBlk_DiatomA	A
SA207044	170213_Smp_Pcx_A	A
SA207045	161107_Blk_MediaBlk_DiatomB	A
SA207046	170821_Smp_Tp35_A	A
SA207047	170213_Smp_Pt_C	A
SA207048	161107_Smp_371_A	A
SA207049	170213_Blk_MediaBlk_Pc55x	A
SA207050	161107_Smp_To_A	A
SA207051	161107_Blk_MediaBlk_DiatomZ	A
SA207052	170821_Smp_Tp28_A	A
SA207053	170821_Smp_1771_A	A
SA207054	170821_Smp_449_A	A
SA207055	161107_Blk_MediaBlk_DiatomYBC	A
SA207056	170821_Blk_FilterBlk_49	A
SA207057	170821_Blk_FilterBlk_N	A
SA207058	170821_Smp_1314_A	A
SA207059	170821_Blk_FilterBlk_71	A
SA207060	161107_Smp_Cy_A	A
SA207061	170821_Smp_2021_A	A
SA207062	161107_Smp_SA30_B	B
SA207063	170213_Smp_SA7_B_rerun	B
SA207064	170213_Smp_SA55_B_rerun	B
SA207065	170117_Smp_SA44_B	B
SA207066	170117_Smp_SA48_B	B
SA207067	170213_Blk_MediaBlk_B	B
SA207068	180227_Smp_Cr_B	B
SA207069	170821_Blk_FilterBlk_Tp28	B
SA207070	170117_Smp_DSS3_B	B
SA207071	161107_Smp_371_B	B
SA207072	180227_Smp_Ca_B	B
SA207073	170213_Smp_Np_C_rerun	B
SA207074	161107_Smp_SA33_B	B
SA207075	170117_Smp_SA11_B	B
SA207076	161107_Smp_Cy_B	B
SA207077	161116_Smp_SA16_B	B
SA207078	170117_Smp_Och_B	B
SA207079	161116_Smp_SA60_B	B
SA207080	170821_Smp_1314P_B	B
SA207081	170821_Smp_1314_B	B
SA207082	161107_Smp_SA42_B	B
SA207083	170821_Smp_As9601_B	B
SA207084	170821_Smp_1771_B	B
SA207085	161107_Smp_2090_B	B
SA207086	161114_Smp_8501_B	B
SA207087	170821_Smp_1545_B	B
SA207088	170821_Smp_Tp10_B	B
SA207089	170821_Smp_449_B	B
SA207090	180227_Smp_3430_B	B
SA207091	180227_Smp_116-1_B	B
SA207092	170821_Smp_Tp28_B	B
SA207093	170117_Smp_SA36_B	B
SA207094	170821_Smp_Tp35_B	B
SA207095	170821_Smp_2021_B	B

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)
Column Temperature:	30
Flow Rate:	0.15 mL/min
Solvent A:	85% acetonitrile/15% water; 10 mM ammonium carbonate
Solvent B:	40% acetonitrile/60% water; 10 mM ammonium carbonate
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)
Column Temperature:	35
Flow Rate:	0.4 mL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
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