Proteomics

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Zebrafish SWATH-MS spectral library to quantify 10,000 proteins

ABSTRACT: 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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Eye, Spleen, Heart, Testis, Ovary, Brain, Intestine, Liver, Muscle

SUBMITTER: Peter Blattmann  

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD010876 | Pride | 2018-12-18

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
Zebrafish_Ensembl91_longesttrx.fasta Fasta
Zebrafish_consensus_library.sptxt Other
Zebrafish_s64_osw_decoy.TraML Other
iprophet.pep.xml Pepxml
sample_annotation_spectral_library.txt Txt
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Publications

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins.

Blattmann Peter P   Stutz Vivienne V   Lizzo Giulia G   Richard Joy J   Gut Philipp P   Aebersold Ruedi R  

Scientific data 20190212

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 prese  ...[more]

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