Summary of Study ST002789

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 PR001738. The data can be accessed directly via it's Project DOI: 10.21228/M82719 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 IDST002789
Study TitleMetabolomic analysis of particulate matter in the NPSG during a 2017 cruise on the R/V Kilo Moana as part of the MESOSCOPE program
Study SummaryTargeted and untargeted analysis of metabolomics samples from the North Pacific Subtropical Gyre taken during the 2017 June/July SCOPE cruise on the R/V Kilo Moana (KM1709) across a mesoscale eddy dipole, with high-resolution depth profile sampling across the DCM in the center of each eddy. Particulate matter was collected on 0.2um filters and extracted using a modified Bligh & Dyer before analysis on a QE Orbitrap. Results show significant changes in the absolute quantity and relative composition of particles in the gyre between anticyclonic and cyclonic eddies.
Institute
University of Washington
DepartmentSchool of Oceanography
LaboratoryIngalls Lab
Last NameKumler
First NameWilliam
Address1501 NE Boat St, Seattle, WA 98105
Emailwkumler@uw.edu
Phone2062216732
Submit Date2023-07-19
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-08-10
Release Version1
William Kumler William Kumler
https://dx.doi.org/10.21228/M82719
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001738
Project DOI:doi: 10.21228/M82719
Project Title:The influence of mesoscale eddy features on marine metabolomic variability in the North Pacific Subtropical Gyre
Project Type:Marine Metabolomics
Project Summary:Mesoscale eddies are a dominant source of variability in the ocean's gyres, often analogized to the "weather" of the sea. They alter the balance between light and nutrients, shifting community composition on both the species and molecular scale. Here, we collected metabolomic samples from across eddy dipoles in the North Pacific Subtropical Gyre to detect and quantify these shifts on a chemical level. The data indicate that metabolites dynamically and robustly track with biological community metrics and result in biochemically distinct particulate matter in cyclonic and anticyclonic eddies.
Institute:University of Washington
Department:School of Oceanography
Laboratory:Ingalls Lab
Last Name:Kumler
First Name:William
Address:1501 NE Boat St, Seattle, WA, 98105, USA
Email:wkumler@uw.edu
Phone:2062216732
Funding Source:Simons Collaboration on Ocean Processes and Ecology, NSF

Subject:

Subject ID:SU002896
Subject Type:Other organism
Subject Species:Natural mixed marine microbial community

Factors:

Subject type: Other organism; Subject species: Natural mixed marine microbial community (Factor headings shown in green)

mb_sample_id local_sample_id Sample_type Station Depth
SA299130170706_Blk_Blk0p2_1.mzMLBlank NA NA
SA299131170706_Blk_Blk0p2_2.mzMLBlank NA NA
SA299132180821_Poo_Day1and2Poo_Half5.mzMLQC Pooled NA NA
SA299133180821_Poo_Day1and2Poo_Half4.mzMLQC Pooled NA NA
SA299134180821_Poo_Day1and2Poo_Half3.mzMLQC Pooled NA NA
SA299135180821_Poo_Day1and2Poo_Half6.mzMLQC Pooled NA NA
SA299136180205_Poo_TruePoo_Full3.mzMLQC Pooled NA NA
SA299137180205_Poo_TruePoo_Half3.mzMLQC Pooled NA NA
SA299138180205_Poo_TruePoo_Half1.mzMLQC Pooled NA NA
SA299139180821_Poo_Day1and2Poo_Half2.mzMLQC Pooled NA NA
SA299140180821_Poo_Day1and2Poo_Half1.mzMLQC Pooled NA NA
SA299141180821_Poo_Day1and2Poo_Full2.mzMLQC Pooled NA NA
SA299142180821_Poo_Day1and2Poo_Full1.mzMLQC Pooled NA NA
SA299143180821_Poo_Day1and2Poo_Full3.mzMLQC Pooled NA NA
SA299144180821_Poo_Day1and2Poo_Full4.mzMLQC Pooled NA NA
SA299145180821_Poo_Day1and2Poo_Full6.mzMLQC Pooled NA NA
SA299146180821_Poo_Day1and2Poo_Full5.mzMLQC Pooled NA NA
SA299147180205_Poo_TruePoo_Full1.mzMLQC Pooled NA NA
SA299148180205_Poo_TruePoo_Half2.mzMLQC Pooled NA NA
SA299149180205_Poo_TruePoo_Full2.mzMLQC Pooled NA NA
SA299150180821_Smp_MS10C2DCM_A.mzMLSample 10 DCM
SA299151180821_Smp_MS10C2DCM_B.mzMLSample 10 DCM
SA299152180821_Smp_MS10C2DCM_C.mzMLSample 10 DCM
SA299153180821_Smp_MS10C2175m_B.mzMLSample 10 Deep
SA299154180821_Smp_MS10C2175m_C.mzMLSample 10 Deep
SA299155180821_Smp_MS10C2175m_A.mzMLSample 10 Deep
SA299156180821_Smp_MS10C215m_C.mzMLSample 10 Surface
SA299157180821_Smp_MS10C215m_B.mzMLSample 10 Surface
SA299158180821_Smp_MS10C215m_A.mzMLSample 10 Surface
SA299159180821_Smp_MS11C2DCM_A.mzMLSample 11 DCM
SA299160180821_Smp_MS11C2DCM_C.mzMLSample 11 DCM
SA299161180821_Smp_MS11C2DCM_B.mzMLSample 11 DCM
SA299162180821_Smp_MS11C2175m_B.mzMLSample 11 Deep
SA299163180821_Smp_MS11C2175m_C.mzMLSample 11 Deep
SA299164180821_Smp_MS11C2175m_A.mzMLSample 11 Deep
SA299165180821_Smp_MS11C215m_C.mzMLSample 11 Surface
SA299166180821_Smp_MS11C215m_A.mzMLSample 11 Surface
SA299167180821_Smp_MS11C215m_B.mzMLSample 11 Surface
SA299168180821_Smp_MS12C1DCM_A.mzMLSample 12 DCM
SA299169180821_Smp_MS12C1DCM_C.mzMLSample 12 DCM
SA299170180821_Smp_MS12C1DCM_B.mzMLSample 12 DCM
SA299171180821_Smp_MS12C1175m_C.mzMLSample 12 Deep
SA299172180821_Smp_MS12C1175m_B.mzMLSample 12 Deep
SA299173180821_Smp_MS12C1175m_A.mzMLSample 12 Deep
SA299174180821_Smp_MS12C115m_A.mzMLSample 12 Surface
SA299175180821_Smp_MS12C115m_C.mzMLSample 12 Surface
SA299176180821_Smp_MS12C115m_B.mzMLSample 12 Surface
SA299177180821_Smp_MS13C2DCM_C.mzMLSample 13 DCM
SA299178180821_Smp_MS13C2DCM_B.mzMLSample 13 DCM
SA299179180821_Smp_MS13C2DCM_A.mzMLSample 13 DCM
SA299180180821_Smp_MS13C2175m_B.mzMLSample 13 Deep
SA299181180821_Smp_MS13C2175m_C.mzMLSample 13 Deep
SA299182180821_Smp_MS13C2175m_A.mzMLSample 13 Deep
SA299183180821_Smp_MS13C315m_A.mzMLSample 13 Surface
SA299184180821_Smp_MS13C315m_B.mzMLSample 13 Surface
SA299185180821_Smp_MS13C315m_C.mzMLSample 13 Surface
SA299186180821_Smp_MS14C2DCM_C.mzMLSample 14 DCM
SA299187180821_Smp_MS14C2DCM_B.mzMLSample 14 DCM
SA299188180821_Smp_MS14C2DCM_A.mzMLSample 14 DCM
SA299189180821_Smp_MS14C2175m_C.mzMLSample 14 Deep
SA299190180821_Smp_MS14C2175m_A.mzMLSample 14 Deep
SA299191180821_Smp_MS14C2175m_B.mzMLSample 14 Deep
SA299192180821_Smp_MS14C215m_A.mzMLSample 14 Surface
SA299193180821_Smp_MS14C215m_C.mzMLSample 14 Surface
SA299194180821_Smp_MS14C215m_B.mzMLSample 14 Surface
SA299195180821_Smp_MS4C1DCM_B.mzMLSample 4 DCM
SA299196180821_Smp_MS4C1DCM_A.mzMLSample 4 DCM
SA299197180821_Smp_MS4C1DCM_C.mzMLSample 4 DCM
SA299198180821_Smp_MS4C1175m_C.mzMLSample 4 Deep
SA299199180821_Smp_MS4C1175m_B.mzMLSample 4 Deep
SA299200180821_Smp_MS4C1175m_A.mzMLSample 4 Deep
SA299201180821_Smp_MS4C115m_A.mzMLSample 4 Surface
SA299202180821_Smp_MS4C115m_B.mzMLSample 4 Surface
SA299203180821_Smp_MS4C115m_C.mzMLSample 4 Surface
SA299204180821_Smp_MS5C1DCM_A.mzMLSample 5 DCM
SA299205180821_Smp_MS5C1DCM_B.mzMLSample 5 DCM
SA299206180821_Smp_MS5C1DCM_C.mzMLSample 5 DCM
SA299207180821_Smp_MS5C1175m_A.mzMLSample 5 Deep
SA299208180821_Smp_MS5C1175m_B.mzMLSample 5 Deep
SA299209180821_Smp_MS5C1175m_C.mzMLSample 5 Deep
SA299210180821_Smp_MS5C115m_C.mzMLSample 5 Surface
SA299211180821_Smp_MS5C115m_B.mzMLSample 5 Surface
SA299212180821_Smp_MS5C115m_A.mzMLSample 5 Surface
SA299213180821_Smp_MS6C3DCM_A.mzMLSample 6 DCM
SA299214180821_Smp_MS6C3DCM_C.mzMLSample 6 DCM
SA299215180821_Smp_MS6C3DCM_B.mzMLSample 6 DCM
SA299216180821_Smp_MS6C3175m_A.mzMLSample 6 Deep
SA299217180821_Smp_MS6C3175m_C.mzMLSample 6 Deep
SA299218180821_Smp_MS6C3175m_B.mzMLSample 6 Deep
SA299219180821_Smp_MS6C315m_C.mzMLSample 6 Surface
SA299220180821_Smp_MS6C315m_A.mzMLSample 6 Surface
SA299221180821_Smp_MS6C315m_B.mzMLSample 6 Surface
SA299222180821_Smp_MS7C1DCM_C.mzMLSample 7 DCM
SA299223180821_Smp_MS7C1DCM_B.mzMLSample 7 DCM
SA299224180821_Smp_MS7C1DCM_A.mzMLSample 7 DCM
SA299225180821_Smp_MS7C1175m_C.mzMLSample 7 Deep
SA299226180821_Smp_MS7C1175m_B.mzMLSample 7 Deep
SA299227180821_Smp_MS7C1175m_A.mzMLSample 7 Deep
SA299228180821_Smp_MS7C115m_A.mzMLSample 7 Surface
SA299229180821_Smp_MS7C115m_B.mzMLSample 7 Surface
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Collection:

Collection ID:CO002889
Collection Summary:Samples were collected aboard the R/V Kilo Moana in June and July 2017. Water was collected with Niskin bottles attached to the CTD from the surface and the deep chlorophyll maximum (DCM), and 175 meters depth. Water was filtered onto a 0.2um pore size filter under gentle vacuum pressure prior to flash-freezing in LN2 before storage at -80 in precombusted aluminum foil. Samples were collected in two stages, the first of which was a transect across the entire eddy dipole from one edge to another while the second stage was a long-term Lagrangian occupation of the eddy centers (L1 = cyclone @ -12cm, L2 = anticyclone @ +25cm). Samples for the transect were collected throughout the day while the eddy center samples were all collected at about 6pm.
Sample Type:Suspended Marine Particulate Matter
Collection Method:CTD Niskin Bottle
Collection Location:North Pacific
Volumeoramount Collected:10L
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002905
Treatment Summary:No experimental manipulations were performed on the samples.

Sample Preparation:

Sampleprep ID:SP002902
Sampleprep Summary:Polar metabolites were extracted using a modified Bligh−Dyer extraction using 1:1 methanol/water and dichloromethane. A methodological blank was extracted and analyzed alongside. Isotope-labeled internal standards were added both before and after the extraction for all samples, blanks, and pooled samples. To evaluate the effect of obscuring variation due to different matrix strengths and analytical drift, pooled samples were run at both full and half concentration (diluted with water) at least three times during the run. This study ran the eddy center samples separately from the eddy transect samples but they were processed together.
Processing Storage Conditions:On ice
Extraction Method:Bligh-Dyer
Extract Storage:-80℃

Combined analysis:

Analysis ID AN004538 AN004539
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Waters Acquity I-Class Waters Acquity I-Class
Column SeQuant ZIC-HILIC (150 x 2.1mm, 5um) SeQuant ZIC-HILIC (150 x 2.1mm, 5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units normalized peak area per liter seawater filtered normalized peak area per liter seawater filtered

Chromatography:

Chromatography ID:CH003409
Chromatography Summary:A SeQuant ZIC-pHILIC column (5 um 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 85:15 water to acetonitrile (Solvent B) at a flow rate of 0.15 mL/min. This column was compared with a Waters UPLC BEH amide and a Millipore cHILIC column; the pHILIC showed superior reproducibility and peak shapes. The column was held at 100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total). The column was maintained at 30 C. The injection volume was 2 µL for samples and standard mixes. When starting a batch, the column was equilibrated at the starting conditions for at least 30 minutes. To improve the performance of the HILIC column, we maintained the same injection volume, kept the instrument running water blanks between samples as necessary, and injected standards in a representative matrix in addition to standards in water. After each batch, the column was flushed with 10 mM ammonium carbonate in 85:15 water to acetonitrile for 20 to 30 minutes.
Instrument Name:Waters Acquity I-Class
Column Name:SeQuant ZIC-HILIC (150 x 2.1mm, 5um)
Column Temperature:30
Flow Gradient:100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total)
Flow Rate:0.15 mL/min
Solvent A:85% acetonitrile/15% water
Solvent B:15% acetonitrile/85% water
Chromatography Type:HILIC

MS:

MS ID:MS004285
Analysis ID:AN004538
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolomic data was collected on a Thermo Q Exactive HF hybrid Orbitrap (QE) mass spectrometer. The capillary and auxiliary gas heater temperatures were maintained at 320°C and 100°C, respectively. The S-lens RF level was kept at 65, the H-ESI voltage was set to 3.3 kV and sheath gas, auxiliary gas, and sweep gas flow rates were set at 16, 3, and 1, respectively. Polarity switching was used with a scan range of 60 to 900 m/z and a resolution of 60,000. Calibration was performed every 3-4 days at a target mass of 200 m/z. All files were then converted to an open-source mzML format and centroided via Proteowizard’s msConvert tool. Skyline was used to for manual integration and QC of quantified data, while XCMS was used with a custom QC method for peak area data and each feature manually reviewed.
Ion Mode:POSITIVE
  
MS ID:MS004286
Analysis ID:AN004539
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolomic data was collected on a Thermo Q Exactive HF hybrid Orbitrap (QE) mass spectrometer. The capillary and auxiliary gas heater temperatures were maintained at 320°C and 100°C, respectively. The S-lens RF level was kept at 65, the H-ESI voltage was set to 3.3 kV and sheath gas, auxiliary gas, and sweep gas flow rates were set at 16, 3, and 1, respectively. Polarity switching was used with a scan range of 60 to 900 m/z and a resolution of 60,000. Calibration was performed every 3-4 days at a target mass of 200 m/z. All files were then converted to an open-source mzML format and centroided via Proteowizard’s msConvert tool. Skyline was used to for manual integration and QC of quantified data, while XCMS was used with a custom QC method for peak area data with the model trained on positive mode data applied to these negative mode results.
Ion Mode:NEGATIVE
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