Dataset: Year 1 orbitrap MZML files

Name: Raw proteome mass spectrometry data (.mzML files) from pacific herring embryos sampled at Semiahmoo Bay between February and April 2022
Published: 2024-11-12
Keywords: herring, proteomics, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.938909.1

Spatial Extent: N:48.992824917812 E:-122.78378231373 S:48.992824917812 W:-122.78378231373

Semiahmoo Spit, WA

Temporal Extent: 2022-02 - 2022-04

Project:

MCA: Utilizing high-throughput proteomics to build a conceptual model of the effects of environmental change on early life stages of genetically diverse herring populations (Herring Proteomics )

Principal Investigator:

Brooke Love (Western Washington University, WWU)

Contact:

Brooke Love (Western Washington University, WWU)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-11-12

Restricted:

Yes

Release Date:

2026-08-01

Validated:

Yes

Current State:

Final no updates expected

Raw proteome mass spectrometry data (.mzML files) from pacific herring embryos sampled at Semiahmoo Bay between February and April 2022

Abstract:

These are the raw data files from 5 cohorts of pacific herring embryos collected from Feb through April of 2022. Embryos were homogenized, and digested for proteomic analysis on a Lumos Orbitrap. Pooled samples were used with narrow window scans for library generation. The purpose of this data set is exploratory analysis for seasonal differences between early life stage proteome of pacific herring. All embryos are believed to be from the Semiahmoo Bay population since the Cherry Point population had no spawn detected in 2022.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2024-11-12	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.938909.1	2024-11-12

Methods & Sampling

Embryos collected with a rake from small boat on 5 dates across three months and kept in a cooler with ambient seawater for 1-5 hours until returned to the lab. 1-5 embryos flash frozen and stored cyogenically for 3-6 months until processing.

Data Processing Description

Embryos were physically broken with a micropestle in a microcentriguge tube, then processed 3x 30 seconds with stainless steel beads in a bullet blender. Homogenate was removed from the bead then sonicated 3x. and digested using trypsin and a standard s-trap protocol. Tubes were dried using a speed vap and reconstituted in water/ACN.

Samples were spiked with Pierce retention time standards and with yeast enolase as a standard in some cases. A 90 minute gradient was run on the LC serving the Lumos.

Data Files

File
938909_v1_orbitrap.csv (Comma Separated Values (.csv), 5.81 KB) MD5:fe97252b745ce72fd108016c244daa5e Primary data file for dataset ID 938909, version 1

Supplemental Files

File
mzml_2023_herring.zip (ZIP Archive (ZIP), 26.46 GB) MD5:bab416f1568db295f90396c9a67483a8 Raw mass spectrometry data (.MzML) files. see inventory file for naming and sampling details of the files.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2219978
NSF Division of Ocean Sciences	OCE-2219978

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: Lumos Orbitrap

Supplied Description:

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
Location	Sampling area: Semiahmoo Bay	unitless	region
Date_Sampling	Sampling date Format: %Y-%m-%d	unitless	date
Latitude	Approximate sample latitude	decimal degrees	lat
Longitude	Approximate sample longitude	decimal degrees	lon
Sample_ID	Sample ID: cohort + sampling id	unitless	sample
Cohort	Cohorts of pacific herring embryos: 1 - 5	unitless	sample_descrip
Replicate	Sample replicate	unitless	replicate
Mass_Spec_Run_Number	Mass spectrometry run number	unitless	sample_descrip
Date_Mass_Spec	Date of spectrometry run Format: %Y-%m-%d	unitless	date
Sample_Type	Description of single sample vs pool samples.	unitless	sample_type
Filename	Filename of .mzml file in supplemental files. File name convention: DateRun_Intrument_project_sampleID_RunNumber	unitless	file_name

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Database

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Dataset: Year 1 orbitrap MZML files