Dataset: Year 1 orbitrap MZML files

Name: Raw proteome mass spectrometry data (.mzML files) from pacific herring embryos sampled at Semiahmoo Bay between January and June 2022.
Published: 2024-09-26
Keywords: herring, proteomics, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:49.001043046141 E:-122.73471658379 S:48.962041497662 W:-122.78635660598

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)

BCO-DMO Data Manager:

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

Version:

Version Date:

2024-09-26

Restricted:

Yes

Validated:

Current State:

Data not available

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

Expand/Collapse All

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.

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

None available yet

Status message

Database

Contribute Data

Dataset: Year 1 orbitrap MZML files