Dataset: Interlab Study 2021

Name: 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
Published: 2021-08-27
Keywords: marine dissolved organic matter, Synechococcus, interlab study, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:32.8663 E:-117.2546 S:32.8663 W:-117.2546

Temporal Extent: 2021-02 - 2021-05

Project:

The Metabolic Response of Coastal Bacteria to Mortality-Derived Phytoplankton Dissolved Organic Matter (MortalityDOM)

Principal Investigator:

Elizabeth Kujawinski (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Krista Longnecker (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-08-27

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

Results from one participating lab in a liquid chromatography–mass spectrometry (LC-MS) inter-lab study of marine dissolved organic matter and algal extracts. These results are from lab number 5 (Kujawinski) from analyses that took place in May of 2021 that used both seawater from Ellen Browning Scripps Memorial Pier, San Diego, CA, and cultures. The dataset from lab number 5 contains three types of files from 68 analytical runs on an Orbitrap Fusion Lumos mass spectrometer. There are three files for each run: one is a 'raw' file that is the vendor-specific format produced by the instrument, the second is an mzML file with only the MS1 peak information generated by ProteoWizard's msConvert tool, and the third type of file is an mzML file with the MS1 and MS2 peak information generated by ProteoWizard's msConvert tool. These are unprocessed data files that are available at MassIVE (http://dx.doi.org/10.25345/C5D25T) in order to allow computational analysis with the Global Natural Product Social Molecular Networking (GNPS) set of networking tools.

Expand/Collapse All

Methods & Sampling

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).

The samples range from 100% seawater to 100% culture. The seawater was collected from the Ellen Browning Scripps Memorial Pier on the 26th of February 2021 between 11:00 and 19:00 PDT. That pier is here: 32.8663° N, 117.2546° W

See Supplemental Files section for further sample preparation procedures and details relevant to all labs participating in the study.

Kujawinski lab (lab 5) parameters:

Massive ID: MSV000087588

Mass Spec Type: Orbitrap Fusion Lumos

LC Type: UHPLC

Column Name: Waters Acquity HSS T3

Column Dimesions:2.1 x 100 mm, 1.8 um, 0.4

Gradient Length [min]: 10

Total Method length [min]: 17

Gradient: "5% to 50% B (7 min), 50% to 99% B (10 min), 99% to 99% B (13min), 5% to 5% B (17Min)"

-->MS1 parameters

Mass Range: 150-1500

MS1 Resolution: 500000

Micro Scans: 1

Max fill time MS1:200

AGC MS1: default

DDA Duty Cycle Time: ~1 sec

-->MS/MS parameters

Mass Range: 150-1500

MS1 Resolution: 120000

MS2 Resolution: 30000

Micro Scans: 1

Max fill time MS1: 100

Max fill time MS2: 100

AGC MS1: default

AGC MS2: default

Stepped collision energy: 20,30,40

MS/MS Threshold Absolute: 2.50E+04

TopN DDA: 5

Dynamic Exclusion: 5

DDA Duty Cycle Time: ~1 sec
Instruments:

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: 1.8m

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.

Data Processing Description

Vendor-specific data files were converted to mzML files using msConvert.

mzML file parameters:

Mass range: 150 to 1500 m/z

MS1 mass resolution: 500000

Max fill time: 200 microseconds

MS1 Automatic Gain Control (AGC) = default

Data Dependent Duty Cycle Time ~ 1 second

Files submitted to MassIVE at the Center for Computational Mass Spectrometry under accession MSV000087588 "DOM LCMS-Interlab Study 2021 Lab5, version 2" (See Related Datasets section for full citation).

Supplemental Files

File
Sample preparation and analysis guide filename: Inter-Lab-Comparison_MS-Settings.pdf (Portable Document Format (.pdf), 83.70 KB) MD5:e958f064598fbb2c10c6389ee39c1bed DOM_Interlab-LCMS study 2021 - Sample preparation and analysis guide (documentation version on 2021-10-08).
Study sample prep, step-to-step pipetting scheme filename: DOM-Interlab-Study_sample-prep-step-to-step.pdf (Portable Document Format (.pdf), 32.57 KB) MD5:5658698499b21bb2664b849c6280c197 DOM Inter-Lab MS/MS study sample preparation, step-to-step pipetting scheme (documentation version on 2021-10-08).
Study sample preparation filename: DOM-Interlab-Study_sample_prep.pdf (Portable Document Format (.pdf), 73.40 KB) MD5:21e7d873db295986d7a125e5943db44c DOM Inter-Lab MS/MS study sample preparation. This document contains sample processing details (documentation version on 2021-10-08).

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1634016

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: Orbitrap Fusion Lumos

Supplied 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 Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic 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.

Parameters

None available yet

Status message

Database

Contribute Data

Dataset: Interlab Study 2021