PXD011006-1

PXD011006 is an original dataset announced via ProteomeXchange.

Title	SRM of geoduck hemolymph peptides to develop biomarkers (Timmins-Schiffman et al. 2017)
Description	Geoduck clams are an increasingly important aquaculture product in the Pacific Northwest of the United States, whilealso holding essential ecological roles in the ecosystem. These long-lived clams are very fecund, but hatchery production of larvae is hindered by the inability to sex a live geoduck, thus resulting in asynchronous spawning of broodstock and unequal sex ratios. During geoduck reproductive maturation, the physiology of the gonad changes from sexually undifferentiated mantle tissue to sex-specific, mature reproductive cells that can be released into the water column. We applied proteomics tools to uncover the cellular mechanisms underlying these physiological changes in the gonad. Sex- and stage-specific proteins were characterized using data dependent acquisition (DDA), or whole proteome profiling, on gonad tissue. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data were leveraged to develop biomarkers of geoduck sex and maturation stage, analyzed with selected reaction monitoring (SRM) in gonad and hemolymph. The SRM assay yielded a reduced suite of peptides that can be used as an efficient assay to non-lethally determine geoduck sex and maturation stage pre-spawning. This is one of a few examples of cutting-edge proteomics being used to develop applicable tools for the aquaculture industry.
HostingRepository	PeptideAtlas
AnnounceDate	2018-09-04
AnnouncementXML	Submission_2018-09-04_09:05:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Emma Timmins-Schiffman
SpeciesList	scientific name: Panopea generosa; NCBI TaxID: 1049056;
ModificationList	No PTMs are included in the dataset
Instrument	TSQ Vantage

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-04 09:01:50	ID requested
⏵ 1	2018-09-04 09:05:42	announced

Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB, Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation. J Proteome Res, 16(9):3298-3309(2017) [pubmed]

curator keyword: selected reaction monitoring, SRM, targeted

Emma Timmins-Schiffman
contact affiliation	University of Washington
contact email	emmats@uw.edu
dataset submitter
Steven Roberts
contact affiliation	University of Washington
contact email	sr320@uw.edu
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI