Dataset: PTR ToF-MS peak tables: Synechococcus WH8102

Name: Mass-to-charge ratio +1 values in microbial cultures (Synechococcus WH8102) detected by proton transfer reaction time-of-flight mass spectrometer in 2021 and 2022
Published: 2022-03-18
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.871678.1

Temporal Extent: 2021-01 - 2022-01

Project:

Interactions between phytoplankton and bacterioplankton mediated by volatile organic compounds (Plankton Interactions and VOC)

Principal Investigator:

Kimberly Halsey (Oregon State University, OSU)

Co-Principal Investigator:

Stephen Giovannoni (Oregon State University, OSU)

BCO-DMO Data Manager:

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

Version:

Version Date:

2022-03-18

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Mass-to-charge ratio +1 values in microbial cultures (Synechococcus WH8102) detected by proton transfer reaction time-of-flight mass spectrometer in 2021 and 2022

Abstract:

Mass-to-charge ratio (m/z) +1 values in microbial cultures (Synechococcus WH8102) were detected by proton transfer reaction time-of-flight mass spectrometer following methods in Moore et al. (2020). doi:10.1111/1462-2920.14861

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-03-18	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.871678.1	2024-02-09

Description

See the "Related Datasets" section for more data from this study with Phaeodactylum tricornutum and cocultures.

PTR ToF-MS in the name of this dataset refers to proton-transfer reaction time-of-flight mass spectrometry (PTR-TOF/MS).

Methods & Sampling

Methodology:

Volatile organic compounds (VOCs) were sampled and measured using dynamic stripping chambers coupled to a proton transfer reaction time-of-flight mass spectrometer (Moore et al. 2020). VOC concentrations (ppbv) are exported directly from the PTR-MS Viewer 3.2.1.2 software (Ionicon Analytik GmbH, Innsbruck, Austria) into .txt files. Air concentrations for each m/z (+1) detected are reported already corrected for mass calibration, transmission efficiencies, and primary ion signals. Data include experiment, culture conditions, and flow conditions. 2-point calibration mode, 0.3 m/z search range, cycle 1000, and using an average of 10 spectra.

Sampling and analytical procedures:
Samples are measured directly from cultures or media blanks. Culture conditions are given as the growth phase (exponential or stationary phase). Cell densities are provided. The protocol is well described in Moore et al. (2020).

Media recipe:

Artificial seawater + 882 μM NO3 + 36.2 μM PO4 + 106 μM Si + 1x f/2 Trace metal mix + 1 x f/2 Vitamin mix

Cell density when VOCs from Synechococcus WH8102 cultures were measured:

Synechococcus_WH8102-A 3.60E+06

Synechococcus_WH8102-B 3.81E+06

Synechococcus_WH8102-C 1.59E+06

Synechococcus_WH8102-D 2.09E+06

Taxon:
Synechococcus, LSID urn:lsid:marinespecies.org:taxname:160572

Data Processing Description

VOC concentrations (ppbv) are exported directly from the PTR-MS Viewer 3.4.4 software (Ionicon Analytik GmbH, Innsbruck, Austria) into .txt files. Air concentrations for each m/z (+1) detected are reported already corrected for mass calibration, transmission efficiencies, and primary ion signals.

BCO-DMO Processing

BCO-DMO Data Manager Processing Notes:
* Data from source file "Synechococcus WH8102 data repositoryv2.xlsx", sheets "Syn_WH8102_data" and "Media_Blank_data", were imported into the BCO-DMO data system and combined into one data table.
* Information from sheet "Sample Information" added to metadata text on this page, and a supplemental data table titled "Sample Information: Synechococcus WH8102" added to the Supplemental File section of this page.
* Values "NA" in the source file were classified as missing data identifiers.
* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions
* Data table unpivoted. Format of the data table converted from wide form where there were data columns for each mz_value containing mz_signals. Converted to long format data table where there is a column "mz_value" and a column "mz_signal."
* Data table sorted by {Sample_Name}{Sample_Replicate}{Sample_Tech}{mz_value}{Time_seconds}
* Missing data values (Blank/Null) values in this dataset are displayed according to the format of data you access. For example, in csv files it will be blank values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as "nd" meaning "no data." See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions

Data Files

File
871678_v1_mz-syn.csv (Comma Separated Values (.csv), 2.84 MB) MD5:bcc1b172b6fc2c70bc7beaad938117f5 Primary data file for dataset ID 871678, version 1

Supplemental Files

File
Sample Information: Synechococcus WH8102 filename: sample_info_Synechococcus.csv (Comma Separated Values (.csv), 430 bytes) MD5:cdd0fa9122bce52861ad05624e6c9117 Additional sample information. Columns: Filename Sample Name Sample type Light (μEin/m2/s) Light: dark Temperature (Celcius) Media Flow (ml/min) Ion Mode Replicates Growth Phase Avg_Cell_Density (cells/ml)

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1948163

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: TOF-1000

Supplied Description:

Proton transfer reaction time of flight mass spectrometer. Ionicon Analytik, Innsbruck, Austria. TOF-1000.

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

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Name	Microbe in culture or coculture with Phaeodactylum tricornutum	unitless	sample
Sample_Name_internal	Internal reference for culture	unitless	sample
Sample_Replicate	Biological replicate	unitless	replicate
Sample_Tech	Technical replicate	unitless	replicate
Time_seconds	time of sampling period (seconds)	seconds (s)	time_elapsed
mz_value	Mass-to-charge (m/z) +1 value identified by PTR-MS. This is the atomic mass plus 1 for a chemical compound detected by the mass spectrometer.	unitless	no_bcodmo_term
mz_signal	Mass-to-charge (m/z) signal	parts per billion by volume (ppbv)	no_bcodmo_term