PXD010869

PXD010869 is an original dataset announced via ProteomeXchange.

Title	Quantification of brain, muscle, and liver using large SWATH-spectral library
Description	Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated for humans and several other organisms, but so far no publicly available library exists for measuring the proteome of zebrafish, a rapidly emerging model system in biomedical research. Here, we present a large zebrafish SWATH spectral library to measure the abundance of 104’185 proteotypic peptides from 10’405 proteins. The library includes proteins expressed in 9 different zebrafish tissues (brain, eye, heart, intestine, liver, muscle, ovaries, spleen, and testes) and provides an important new resource to quantify 40% of the protein-coding zebrafish genes. We employ this resource to quantify the proteome across brain, muscle, and liver and characterize divergent expression levels of paralogous proteins in different tissues.
HostingRepository	PRIDE
AnnounceDate	2018-12-18
AnnouncementXML	Submission_2019-05-31_02:27:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Blattmann
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-27 01:42:51	ID requested
1	2018-12-18 11:24:08	announced
⏵ 2	2019-05-31 02:27:03	announced	Updated publication reference for PubMed record(s): 30747917.

Blattmann P, Stutz V, Lizzo G, Richard J, Gut P, Aebersold R, Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. Sci Data, 6():190011(2019) [pubmed]

curator keyword: Biological

submitter keyword: Zebrafish, brain, liver, muscle

Ruedi Aebersold
contact affiliation	1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland 2 Faculty of Science, University of Zurich, Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Peter Blattmann
contact affiliation	ETH Zurich
contact email	blattmann@imsb.biol.ethz.ch
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/2018/12/PXD010869

PRIDE project URI

• PRIDE
  1. PXD010869
     1. Label: PRIDE project
     2. Name: Quantification of brain, muscle, and liver using large SWATH-spectral library