Dataset: PTR ToF-MS peak tables: Phaeodactylum tricornutum and cocultures

Name: Mass-to-charge ratio +1 values in microbial cultures (Phaeodactylum tricornutum and cocultures) 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.871602.1

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 (Phaeodactylum tricornutum and cocultures) 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 (Phaeodactylum tricornutum and cocultures) 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.871602.1	2024-02-09

Description

See the "Related Datasets" section for more data from this study with Synechococcus WH8102.

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

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 "P.tricorn and cocultures data repositoryv3.xlsx", all sheets starting with name "Sample_*", 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: Phaeodactylum tricornutum and cocultures" 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
* After discussion with the submitter, sample name "SatppiaARW1T_PT_coculture" changed to "StappiaARW1T_PT_coculture"
* taxa and taxon ids associated with each sample name reviewed by submitter and attached as a supplemental file.
* Time_seconds rounded to tenth decimal place.

Data Files

File
871602_v1_mz-p-trico-and-cocultures.csv (Comma Separated Values (.csv), 34.77 MB) MD5:3194ce4d3ac6d63f33d718e7e8fcb325 Primary data file for dataset ID 871602, version 1

Supplemental Files

File

Sample Information: Phaeodactylum tricornutum and cocultures
filename: sample_info_P_trico_adn_cocultures.csv

(Comma Separated Values (.csv), 1.12 KB)
MD5:32b7297984e4de8c9bbe5d19c4b6824c

Additional sample metadata.

Columns:

Filename
Sample Name
Sample type
Light (μEin/m2/s)
Light: dark
Temperature (Celcius)
Media
Flow (ml/min)
Ion Mode
Replicates
Growth Phase
Cell_density (Cells/ml)

Taxon list with identifiers
filename: taxon_ids.csv

(Comma Separated Values (.csv), 669 bytes)
MD5:b756ac068ba04f5556972098eaac8576

Table with the sample name as it appears in the dataset, the associated taxon and identifiers.

Columns:

name_in_dataset, Sample name as it appears in the dataset
taxon, taxon associated with the name in the dataset
AphiaID, taxon identifier for the taxon. Aphia ID, see World Register of Marine Speices (WoRMS) for more information.
LSID, Lifescience Identifier for the taxon

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