http://lod.bco-dmo.org/id/dataset/859694
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2021-08-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Results from lab number 5 from an LCMS inter-lab study of marine dissolved organic matter and algal extracts from analyses in May of 2021 that used both San Diego, CA seawater and laboratory cultures
2021-08-27
publication
2021-08-27
revision
BCO-DMO Linked Data URI
2021-08-27
creation
http://lod.bco-dmo.org/id/dataset/859694
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
principalInvestigator
Krista Longnecker
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Kujawinski, E., Longnecker, K. (2021) Results from lab number 5 from an LCMS inter-lab study of marine dissolved organic matter and algal extracts from analyses in May of 2021 that used both San Diego, CA seawater and laboratory cultures. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-08-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/859694 [access date]
Methods and Sampling: <p>Samples were provided by Jeffrey Hawkes from Uppsala University as part of an inter-lab comparison study which is being run by Hawkes, Daniel Petras (University of Tbingen), and Carsten Simon (ETH Zurich). The seven samples being analyzed include a quality control sample, a blank, a marine sample, an algal lysate, and three samples that are a combination of the marine sample and the algal lysate (A45M : 450 ppm A and 4500 ppm M; A15M: 150 ppm A and 4500 ppm M; A5M: 50 ppm A and 4500 ppm M).<br />
<br />
The samples range from 100% seawater to 100% culture. The seawater was collected from the Ellen Browning Scripps Memorial&nbsp;Pier on the 26th of February 2021 between 11:00 and 19:00 PDT. That pier is here: 32.8663° N, 117.2546° W</p>
<p>See Supplemental Files section for further sample preparation procedures and details relevant to all labs participating in the study.<br />
<br />
Kujawinski lab (lab 5) parameters:</p>
<div>
<div>Massive ID: MSV000087588</div>
<div>Mass Spec Type: Orbitrap Fusion Lumos</div>
<div>LC Type: UHPLC</div>
<div>Column Name: Waters Acquity HSS T3</div>
<div>Column Dimesions:2.1 x 100 mm, 1.8 um, 0.4</div>
<div>Gradient Length [min]: 10</div>
<div>Total Method length [min]: 17</div>
<div>Gradient: "5% to 50% B&nbsp; (7 min), 50% to 99% B (10 min), 99% to 99% B (13min), 5% to 5% B (17Min)"</div>
<div>&nbsp;</div>
<div>--&gt;MS1 parameters</div>
<div>Mass Range: 150-1500</div>
<div>MS1 Resolution: 500000</div>
<div>Micro Scans: 1</div>
<div>Max fill time MS1:200</div>
<div>AGC MS1: default</div>
<div>DDA Duty Cycle Time: ~1 sec</div>
<div>&nbsp;</div>
<div>--&gt;MS/MS parameters</div>
<div>Mass Range: 150-1500</div>
<div>MS1 Resolution: 120000</div>
<div>MS2 Resolution: 30000</div>
<div>Micro Scans: 1</div>
<div>Max fill time MS1: 100</div>
<div>Max fill time MS2: 100</div>
<div>AGC MS1: default</div>
<div>AGC MS2: default</div>
<div>Stepped collision energy: 20,30,40</div>
<div>MS/MS Threshold Absolute: 2.50E+04</div>
<div>TopN DDA: 5</div>
<div>Dynamic Exclusion: 5</div>
<div>DDA Duty Cycle Time: ~1 sec
<p>Instruments:&nbsp;</p>
<div>The samples were analyzed on a Orbitrap Fusion Lumos. The instrument parameters were as follows:&nbsp;</div>
<div>Stationary phase: Waters Acquity HSS T3 column with 2.1 mm x 100 mm.&nbsp;</div>
<div>Particle size: 1.8m&nbsp;</div>
<div>Mobile phase: LC-MS grade water (A), acetonitrile (B) with 0.1% formic acid (FA) each.</div>
<div>Gradient: Start at 5% B, increase to 50% B at 7 min, increase to 99% B at 10 min, 3 min washout phase at 99% B, 4 min equilibration phase at 5% B (method length = 17 min).&nbsp;</div>
<div>Flow rate: 0.4 mL/min with a 5 ul injection.</div>
</div>
</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1634016 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1634016
completed
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
508-289-3493
266 Woods Hole Rd. MS #4
Woods Hole
MA
02543
USA
ekujawinski@whoi.edu
pointOfContact
Krista Longnecker
Woods Hole Oceanographic Institution
508-289-2824
266 Woods Hole Road MS# 04
Woods Hole
MA
02543
USA
klongnecker@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Orbitrap Fusion Lumos
theme
None, User defined
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
The Metabolic Response of Coastal Bacteria to Mortality-Derived Phytoplankton Dissolved Organic Matter
https://osprey.bco-dmo.org/project/854100
The Metabolic Response of Coastal Bacteria to Mortality-Derived Phytoplankton Dissolved Organic Matter
<p><em>NSF Award Abstract:</em><br />
Microbes interact with one another through the exchange of chemicals dissolved in their surrounding waters. Decades of biochemical research have identified a small suite of chemicals that are required by microbes for growth and well-being. This limited suite is now being expanded with novel analytical tools based on mass spectrometry. In this project, the focus will be on chemicals that are released during the death of microbes, with particular attention paid to burst cells after viral infections and to the remnants of cells after grazing by protozoa (single celled organisms). These chemicals are not intentionally released by their producers, but they can still affect the growth and well-being of nearby bacteria and in turn the bacteria's ability to convert these molecules to carbon dioxide. The proposed comparison of the types and reactivities of chemicals released during the death of a brown tide alga will help improve models of carbon cycling in the coastal ocean. Two graduate students will be supported directly by this project. The proponent plans to teach two classes, one a mass spectrometry course, the other an environmental metabolomics course. It is anticipated that as part of the evolution of the metabolomics course, data-training for metabolomics would become part of the course.</p>
<p>Microbial consortia are exquisitely sensitive to chemical changes in their surroundings and the diversity of microbial communities evolves with the composition of available growth substrates and nutrients. Thus, interactions between microbes, through the milieu of dissolved organic matter (DOM), lie at the heart of the global carbon cycle and thus merit significant study and investigation. This project focuses on the molecules that are released during microbial mortality through viral lysis or protozoan grazing. Using novel mass spectrometry-based tools, this project links the composition of dissolved organic matter derived from microbial mortality with the ability of heterotrophic bacteria to remineralize these substrates. Metabolic parameters and carbon transformation rates will be determined as a function of DOM source to assess the impact of DOM type on microbial physiology and carbon turnover. Laboratory results from model organisms will be compared to field settings where the model organisms dominate planktonic communities. The project will generate a suite of molecules that can be used in future experiments as markers of microbial mortality and will provide quantitative comparisons between the reactivity of viral lysate and grazer-derived DOM. These results will support improved parameterizations of microbial networks and their impact on the global carbon cycle.</p>
MortalityDOM
largerWorkCitation
project
eng; USA
oceans
-117.2546
-117.2546
32.8663
32.8663
2021-02-26
2021-05-01
Laboratory
0
BCO-DMO catalogue of parameters from Results from lab number 5 from an LCMS inter-lab study of marine dissolved organic matter and algal extracts from analyses in May of 2021 that used both San Diego, CA seawater and laboratory cultures
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
33352
https://datadocs.bco-dmo.org/docs/305/MortalityDOM/859694/1/data_docs/DOM-Interlab-Study_sample-prep-step-to-step.pdf
Study sample prep, step-to-step pipetting scheme
DOM Inter-Lab MS/MS study sample preparation, step-to-step pipetting scheme (documentation version on 2021-10-08).
download
75166
https://datadocs.bco-dmo.org/docs/305/MortalityDOM/859694/1/data_docs/DOM-Interlab-Study_sample_prep.pdf
Study sample preparation
DOM Inter-Lab MS/MS study sample preparation.
This document contains sample processing details (documentation version on 2021-10-08).
download
85706
https://datadocs.bco-dmo.org/docs/305/MortalityDOM/859694/1/data_docs/Inter-Lab-Comparison_MS-Settings.pdf
Sample preparation and analysis guide
DOM_Interlab-LCMS study 2021 - Sample preparation and analysis guide (documentation version on 2021-10-08).
download
https://osprey.bco-dmo.org/dataset/859694/data/download
download
onLine
dataset
<p>Samples were provided by Jeffrey Hawkes from Uppsala University as part of an inter-lab comparison study which is being run by Hawkes, Daniel Petras (University of Tbingen), and Carsten Simon (ETH Zurich). The seven samples being analyzed include a quality control sample, a blank, a marine sample, an algal lysate, and three samples that are a combination of the marine sample and the algal lysate (A45M : 450 ppm A and 4500 ppm M; A15M: 150 ppm A and 4500 ppm M; A5M: 50 ppm A and 4500 ppm M).<br />
<br />
The samples range from 100% seawater to 100% culture. The seawater was collected from the Ellen Browning Scripps Memorial&nbsp;Pier on the 26th of February 2021 between 11:00 and 19:00 PDT. That pier is here: 32.8663° N, 117.2546° W</p>
<p>See Supplemental Files section for further sample preparation procedures and details relevant to all labs participating in the study.<br />
<br />
Kujawinski lab (lab 5) parameters:</p>
<div>
<div>Massive ID: MSV000087588</div>
<div>Mass Spec Type: Orbitrap Fusion Lumos</div>
<div>LC Type: UHPLC</div>
<div>Column Name: Waters Acquity HSS T3</div>
<div>Column Dimesions:2.1 x 100 mm, 1.8 um, 0.4</div>
<div>Gradient Length [min]: 10</div>
<div>Total Method length [min]: 17</div>
<div>Gradient: "5% to 50% B&nbsp; (7 min), 50% to 99% B (10 min), 99% to 99% B (13min), 5% to 5% B (17Min)"</div>
<div>&nbsp;</div>
<div>--&gt;MS1 parameters</div>
<div>Mass Range: 150-1500</div>
<div>MS1 Resolution: 500000</div>
<div>Micro Scans: 1</div>
<div>Max fill time MS1:200</div>
<div>AGC MS1: default</div>
<div>DDA Duty Cycle Time: ~1 sec</div>
<div>&nbsp;</div>
<div>--&gt;MS/MS parameters</div>
<div>Mass Range: 150-1500</div>
<div>MS1 Resolution: 120000</div>
<div>MS2 Resolution: 30000</div>
<div>Micro Scans: 1</div>
<div>Max fill time MS1: 100</div>
<div>Max fill time MS2: 100</div>
<div>AGC MS1: default</div>
<div>AGC MS2: default</div>
<div>Stepped collision energy: 20,30,40</div>
<div>MS/MS Threshold Absolute: 2.50E+04</div>
<div>TopN DDA: 5</div>
<div>Dynamic Exclusion: 5</div>
<div>DDA Duty Cycle Time: ~1 sec
<p>Instruments:&nbsp;</p>
<div>The samples were analyzed on a Orbitrap Fusion Lumos. The instrument parameters were as follows:&nbsp;</div>
<div>Stationary phase: Waters Acquity HSS T3 column with 2.1 mm x 100 mm.&nbsp;</div>
<div>Particle size: 1.8m&nbsp;</div>
<div>Mobile phase: LC-MS grade water (A), acetonitrile (B) with 0.1% formic acid (FA) each.</div>
<div>Gradient: Start at 5% B, increase to 50% B at 7 min, increase to 99% B at 10 min, 3 min washout phase at 99% B, 4 min equilibration phase at 5% B (method length = 17 min).&nbsp;</div>
<div>Flow rate: 0.4 mL/min with a 5 ul injection.</div>
</div>
</div>
Specified by the Principal Investigator(s)
<p>Vendor-specific data files were converted to mzML files using msConvert.<br />
<br />
mzML file parameters:</p>
<div>Mass range: 150 to 1500 m/z</div>
<div>MS1 mass resolution: 500000</div>
<div>Max fill time: 200 microseconds</div>
<div>MS1 Automatic Gain Control (AGC) = default</div>
<div>Data Dependent Duty Cycle Time ~ 1 second<br />
<br />
Files submitted to&nbsp;MassIVE at the&nbsp;Center for Computational Mass Spectrometry under accession MSV000087588 "DOM LCMS-Interlab Study 2021 Lab5, version 2" (See Related Datasets section for full citation).</div>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Orbitrap Fusion Lumos
Orbitrap Fusion Lumos
PI Supplied Instrument Name: Orbitrap Fusion Lumos PI Supplied Instrument Description:The samples were analyzed on a Orbitrap Fusion Lumos. The instrument parameters were as follows:
Stationary phase: Waters Acquity HSS T3 column with 2.1 mm x 100 mm.
Particle size: 1.8µm
Mobile phase: LC-MS grade water (A), acetonitrile (B) with 0.1% formic acid (FA) each.
Gradient: Start at 5% B, increase to 50% B at 7 min, increase to 99% B at 10 min, 3 min washout phase at 99% B, 4 min equilibration phase at 5% B (method length = 17 min).
Flow rate: 0.4 mL/min with a 5 ul injection. Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/