PXD020366

PXD020366 is an original dataset announced via ProteomeXchange.

Title	Identifying candidate markers of domoic acid toxicosis in undepleted plasma from California sea lions (Zalophus californianus)
Description	This data is a re-analysis of samples used in a prior study (doi:10.1371/journal.pone.0123295) evaluating plasma candidate biomarkers of chronic domoic acid toxicosis (DAT) in California sea lions (Zalophus californianus). The previous study used 2D-gel electrophoresis to analyze plasma from a training (n = 32; 12 DAT and 20 non-DAT) and validation set (n = 20; 7 DAT and 13 non-DAT). Using spot intensity followed by in-gel digestion and LC-MS/MS, decreased ApoE was identified and qualified as a classifier of chronic DAT. The current analysis is from 31 of these samples (14 DAT and 17 non-DAT), since some samples were no longer available or had been through too many freeze/thaw cycles and were no longer suitable for robust analysis. This subset of 31 undepleted plasma samples was analyzed using shotgun proteomics with a tribrid mass spectrometer, and searching was performed with the recently completed California sea lion genome (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Zalophus_californianus/100/). Using MS1-based label-free methods we were able to identify candidate markers of chronic DAT, such as decreasing ApoE, ApoC-III and ApoB-100. We expect other analytical pipelines could be used to analyze this data, and we deliberately collected the MS1 and MS2 at high resolution to enable spectral library creation for approaches such as data-independent acquisition, which may be used in follow-up studies.
HostingRepository	PRIDE
AnnounceDate	2020-07-17
AnnouncementXML	Submission_2020-07-16_17:41:28.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020366
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Benjamin Neely
SpeciesList	scientific name: Zalophus californianus; NCBI TaxID: 9704;
ModificationList	2-pyrrolidone-5-carboxylic acid (Gln); monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-14 17:36:14	ID requested
⏵ 1	2020-07-16 17:41:28	announced

Dataset with its publication pending

submitter keyword: California sea lion, domoic acid, plasma, LC-MSMS

Iliana M. Claudio, Jackson S. Eberwein, Alison M. Bland, Michael G. Janech, Benjamin A. Neely
contact affiliation	NIST Charleston
contact email	benjamin.neely@nist.gov
lab head
Benjamin Neely
contact affiliation	National Institute of Standards and Technology
contact email	benjamin.neely@nist.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020366
     1. Label: PRIDE project
     2. Name: Identifying candidate markers of domoic acid toxicosis in undepleted plasma from California sea lions (Zalophus californianus)