PXD023970

PXD023970 is an original dataset announced via ProteomeXchange.

Title	Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Heart and Blood: the beginning of a comprehensive lake trout protein database
Description	Lake trout (Salvelinus namaycush) are a top-predator species in the Laurentian Great Lakes that are often used as bioindicators of chemical stressors in the ecosystem. Although many studies are done using these fish to determine concentrations of stressors like legacy persistent, bioaccumulative and toxic chemicals, there are currently no proteomic studies on the biological effects these stressors have on the ecosystem. This lack of proteomic studies on Great Lakes lake trout is because there is currently no complete, comprehensive protein database for this species. In this research, we aimed to use proteomic methods and established protein databases from NCBI and UniProtKB to identify potential proteins in the lake trout species. The current study utilized heart tissue and blood from two separate lake trout. Our previous published work on the lake trout liver revealed 4,194 potential protein hits in the NCBI databases and 3,811 potential protein hits in the UniProtKB databases. In the current study, using the NCBI databases we identified 838 potential protein hits for the heart and 580 potential protein hits for the blood of the first lake trout (biological replicate 1). In the second lake trout (biological replicate 2), using the NCBI databases we identified 1,180 potential protein hits for the heart and 561 potential protein hits for the blood. Similar results were obtained using the UniProtKB databases. This study builds on our previous work by continuing to build the first comprehensive lake trout protein database. Through this investigation, we are also able to make observations as to protein homology through evolutionary relationships.
HostingRepository	PRIDE
AnnounceDate	2021-12-30
AnnouncementXML	Submission_2021-12-30_15:19:42.965.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emmalyn Dupree
SpeciesList	scientific name: Salvelinus namaycush; NCBI TaxID: 8040;
ModificationList	No PTMs are included in the dataset
Instrument	Xevo G2 Q-Tof

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-03 08:27:26	ID requested
⏵ 1	2021-12-30 15:19:43	announced

Dupree EJ, Manzoor Z, Alwine S, Crimmins BS, Holsen TM, Darie CC, Proteomic analysis of the lake trout (Salvelinus namaycush) heart and blood: The beginning of a comprehensive lake trout protein database. Proteomics, 22(4):e2100146(2022) [pubmed]

submitter keyword: proteogenomics, proteomics, lake trout, salvelinus namaycush

Costel C Darie
contact affiliation	Associate Professor & Lead, Biochemistry & Proteomics Group Department of Chemistry & Biomolecular Science, Clarkson University
contact email	cdarie@clarkson.edu
lab head
Emmalyn Dupree
contact affiliation	Clarkson University
contact email	dupreeej@clarkson.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD023970

PRIDE project URI

• PRIDE
  1. PXD023970
     1. Label: PRIDE project
     2. Name: Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Heart and Blood: the beginning of a comprehensive lake trout protein database