PXD000368

PXD000368 is an original dataset announced via ProteomeXchange.

Title	Grayling Pleiotropy on plastic adaptive protein expression change
Description	We studied a Norwegian metapopulation of grayling, a spring-spawning freshwater salmonid fish with high homing propensity that has undergone contemporary evolution of early life-history in response to temperature. Samples derived from four spawning sites in four grayling sub-populations in Lake Lesjaskogsvatnet (62 14'N 8 25'E) in southern Norway. Adult grayling were captured at the four spawning sites, stripped of gametes and fertilized eggs were reared in two temperature treatments in common garden conditions as to represent lower and upper temperatures experienced by developing grayling larvae in nature. Proteins were isolated using a standard sodium dodecyl sulphate (SDS)-based extraction method. For trypsin digestion and peptide-level iTRAQ labeling, samples were peptide-labeled with isobaric tags by iTRAQ reagents (4-plex, Applied Biosystems) following the manufacturer's instructions. To clean and fractionate each sample we employed an isotope coded affinity tag procedure (ICAT) using the ICAT Cation Exchange Buffer Pack - Cation Exchange Cartridge system (Applied Biosystems). Four peptide fractions were collected using four concentrations of the elution buffer (50 mM, 100 mM, 150 mM, and 350 mM KH2PO4). Peptides were desalted using C18 macrospin columns (The Nest Group, Southborough, MA). For LC-MS/MS, peptides were separated by reversed-phase chromatography using an Easy-nLC II nanoflow system connected to an Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Bremen, Germany). Peptides were separated at a flow rate of 300 nl/min with 102 min gradients as follows: initially 2 % B to 25% B (60 min), 40% B (90 min), and 100% B (92-102 min). Protein identification and quantification were done using the ProteinPilotTM v.4 program (Applied Biosystems). In the parameters we selected the Paragon method, iodoacetamide for cys alkylation, trypsin for digestion, thorough ID for search effort, biological modifications and amino acid substitutions for ID focus, and bias correction in quantification. As a search database we used all Atlantic salmon (Salmo salar) submitted in the UniProt database (www.uniprot.org) up to March 2012. To evaluate the accuracy of the quantification method, we also did a pilot experiment. We spiked the six-protein mix provided with the iTRAQ kit in ratios 1:3:10 in samples that contained an equal amount of protein extract from a grayling embryo. Then we labeled each sample with a different isobaric tag (114:115:116, respectively). The aim was to employ the proposed methodology to quantify a subset of proteins that change across samples in a cloud of background proteins that remain unchanged and these data are also provided in the dataset.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:47:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Spiros Papakostas
SpeciesList	scientific name: Thymallus thymallus (Grayling) (Salmo thymallus); NCBI TaxID: 36185;
ModificationList	iTRAQ8plex
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-26 09:13:53	ID requested
1	2014-05-28 11:36:32	announced
2	2014-06-04 07:20:30	announced	Updated publication reference for PubMed record(s): 24892934.
⏵ 3	2014-07-24 03:47:31	announced	Updated project metadata.

Papakostas S, V, ø, llestad LA, Bruneaux M, Aykanat T, Vanoverbeke J, Ning M, Primmer CR, Leder EH, Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions. Nat Commun, 5():4071(2014) [pubmed]

curator keyword: Biological

submitter keyword: rapid evolution, local adaptation, thermal adaptation, early-life history, salmonids, iTRAQ, OrbitrapVelos

Spiros Papakostas
contact affiliation	Department of Biology
contact email	spiros.papakostas@utu.fi
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/2014/05/PXD000368

PRIDE project URI

• PRIDE
  1. PXD000368
     1. Label: PRIDE project
     2. Name: Grayling Pleiotropy on plastic adaptive protein expression change