Summary of Study ST002788
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.
| Study ID | ST002788 |
| Study Title | Metabolomic analysis of particulate matter in the NPSG during a 2018 cruise on the R/V Falkor |
| Study Summary | Targeted and untargeted analysis of metabolomics samples from the North Pacific Subtropical Gyre taken during the 2018 March/April SCOPE cruise on the R/V Falkor (FK180310) across a mesoscale eddy dipole. 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 |
| Department | School of Oceanography |
| Laboratory | Ingalls Lab |
| Last Name | Kumler |
| First Name | William |
| Address | 1501 NE Boat St, Seattle, WA 98105 |
| wkumler@uw.edu | |
| Phone | 2062216732 |
| Submit Date | 2023-07-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-08-10 |
| Release Version | 1 |
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: | SU002895 |
| 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 | Absolute_depth | Sea_level_anomaly |
|---|---|---|---|---|---|---|
| SA299089 | 190715_Blk_KM1906U14-Blk_C.mzML | Blank | NA | NA | NA | NA |
| SA299090 | 190715_Poo_TruePooFK180310_Full2.mzML | QC Pooled | NA | NA | NA | NA |
| SA299091 | 190715_Poo_TruePooFK180310_Half3.mzML | QC Pooled | NA | NA | NA | NA |
| SA299092 | 190715_Poo_TruePooFK180310_Full3.mzML | QC Pooled | NA | NA | NA | NA |
| SA299093 | 190715_Poo_TruePooFK180310_Full1.mzML | QC Pooled | NA | NA | NA | NA |
| SA299094 | 190715_Poo_TruePooFK180310_Half1.mzML | QC Pooled | NA | NA | NA | NA |
| SA299095 | 190715_Poo_TruePooFK180310_Half2.mzML | QC Pooled | NA | NA | NA | NA |
| SA299096 | 190715_Smp_FK180310S62C1-DCM_A.mzML | Sample | 62 | DCM | 98 | -13.6 |
| SA299097 | 190715_Smp_FK180310S62C1-DCM_C.mzML | Sample | 62 | DCM | 98 | -13.6 |
| SA299098 | 190715_Smp_FK180310S62C1-DCM_B.mzML | Sample | 62 | DCM | 98 | -13.6 |
| SA299099 | 190715_Smp_FK180310S62C1-25m_B.mzML | Sample | 62 | Surface | 25 | -12.48 |
| SA299100 | 190715_Smp_FK180310S62C1-25m_A.mzML | Sample | 62 | Surface | 25 | -12.48 |
| SA299101 | 190715_Smp_FK180310S62C1-25m_C.mzML | Sample | 62 | Surface | 25 | -12.48 |
| SA299102 | 190715_Smp_FK180310S64C1-DCM_C.mzML | Sample | 64 | DCM | 115 | -12.1225 |
| SA299103 | 190715_Smp_FK180310S64C1-DCM_A.mzML | Sample | 64 | DCM | 115 | -12.1225 |
| SA299104 | 190715_Smp_FK180310S64C1-DCM_B.mzML | Sample | 64 | DCM | 115 | -12.1225 |
| SA299105 | 190715_Smp_FK180310S64C1-25m_B.mzML | Sample | 64 | Surface | 25 | -12.48 |
| SA299106 | 190715_Smp_FK180310S64C1-25m_C.mzML | Sample | 64 | Surface | 25 | -12.48 |
| SA299107 | 190715_Smp_FK180310S64C1-25m_A.mzML | Sample | 64 | Surface | 25 | -12.48 |
| SA299108 | 190715_Smp_FK180310S77C1-DCM_B.mzML | Sample | 77 | DCM | 125 | 19.87 |
| SA299109 | 190715_Smp_FK180310S77C1-DCM_A.mzML | Sample | 77 | DCM | 125 | 19.87 |
| SA299110 | 190715_Smp_FK180310S77C1-DCM_C.mzML | Sample | 77 | DCM | 125 | 19.87 |
| SA299111 | 190715_Smp_FK180310S77C1-25m_B.mzML | Sample | 77 | Surface | 25 | 20.8044 |
| SA299112 | 190715_Smp_FK180310S77C1-25m_C.mzML | Sample | 77 | Surface | 25 | 20.8044 |
| SA299113 | 190715_Smp_FK180310S77C1-25m_A.mzML | Sample | 77 | Surface | 25 | 20.8044 |
| SA299114 | 190715_Smp_FK180310S80C1-DCM_B.mzML | Sample | 80 | DCM | 120 | 21.03 |
| SA299115 | 190715_Smp_FK180310S80C1-DCM_A.mzML | Sample | 80 | DCM | 120 | 21.03 |
| SA299116 | 190715_Smp_FK180310S80C1-DCM_C.mzML | Sample | 80 | DCM | 120 | 21.03 |
| SA299117 | 190715_Smp_FK180310S80C1-25m_B.mzML | Sample | 80 | Surface | 25 | 20.8044 |
| SA299118 | 190715_Smp_FK180310S80C1-25m_C.mzML | Sample | 80 | Surface | 25 | 20.8044 |
| SA299119 | 190715_Smp_FK180310S80C1-25m_A.mzML | Sample | 80 | Surface | 25 | 20.8044 |
| SA299120 | 190715_Std_4uMStdsMix2InMatrix_2.mzML | Standard mix | NA | NA | NA | NA |
| SA299121 | 190715_Std_H2OinMatrix_1.mzML | Standard mix | NA | NA | NA | NA |
| SA299122 | 190715_Std_H2OinMatrix_2.mzML | Standard mix | NA | NA | NA | NA |
| SA299123 | 190715_Std_4uMStdsMix2InMatrix_1.mzML | Standard mix | NA | NA | NA | NA |
| SA299124 | 190715_Std_4uMStdsMix1InMatrix_1.mzML | Standard mix | NA | NA | NA | NA |
| SA299125 | 190715_Std_4uMStdsMix1InH2O_1.mzML | Standard mix | NA | NA | NA | NA |
| SA299126 | 190715_Std_4uMStdsMix1InH2O_2.mzML | Standard mix | NA | NA | NA | NA |
| SA299127 | 190715_Std_4uMStdsMix1InMatrix_2.mzML | Standard mix | NA | NA | NA | NA |
| SA299128 | 190715_Std_4uMStdsMix2InH2O_1.mzML | Standard mix | NA | NA | NA | NA |
| SA299129 | 190715_Std_4uMStdsMix2InH2O_2.mzML | Standard mix | NA | NA | NA | NA |
| Showing results 1 to 41 of 41 |
Collection:
| Collection ID: | CO002888 |
| Collection Summary: | Samples were collected aboard the R/V Falkor in March and April 2018. Water was collected with Niskin bottles attached to the CTD from the surface and the deep chlorophyll maximum (DCM) in both the morning (~6AM) and evening (~6PM). 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 from two locations, one in a cyclonic eddy (-13cm, stations 62 and 64) and one in an anticyclonic eddy (+20cm, stations 77 and 80) three days apart. |
| Sample Type: | Suspended Marine Particulate Matter |
| Collection Method: | CTD Niskin Bottle |
| Collection Location: | North Pacific |
| Volumeoramount Collected: | 10L |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002904 |
| Treatment Summary: | No experimental manipulations were performed on the samples. |
Sample Preparation:
| Sampleprep ID: | SP002901 |
| 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) three times during the run. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Bligh-Dyer |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004536 | AN004537 |
|---|---|---|
| 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 of seawater filtered |
Chromatography:
| Chromatography ID: | CH003408 |
| 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: | MS004283 |
| Analysis ID: | AN004536 |
| 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: | MS004284 |
| Analysis ID: | AN004537 |
| 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 |
