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, ovary, spleen, and testis) 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. Data are available via ProteomeXchange (PXD010876, PXD010869) and SWATHAtlas (PASS01237).
Highlights
Background & SummaryProteins execute most cellular processes and define the phenotype of cells and tissues[1]
SWATH-MS requires a spectral library containing SWATH assay coordinates to extract the peptide quantities from the multiplexed mass spectrometry data[5,11,12]. Alternative approaches such as DIA-Umpire or PECAN exist to query mass spectrometry data acquired in data-independent acquisition (DIA) mode without the need of a spectral library, but until now they have proven less sensitive[10,13,14]
Whereas a study-specific SWATH spectral library can be generated with moderate effort, using large previously assembled spectral libraries that are shared by the community has, among other things, the advantage of reducing the amount of sample and measurement time typically by 50% and of supporting protein identifications with a consistent set of reference spectra
Summary
Proteins execute most cellular processes and define the phenotype of cells and tissues[1]. SWATH-MS is a mass spectrometry method that can be employed to reproducibly quantify the proteome across a large number of biological samples as it combines data-independent acquisition (DIA) with a peptide-centric data query strategy[5,6,7,8]. This proteomic method has been systematically benchmarked and has shown to produce highly reproducible results when measuring the same samples in various laboratories and when analyzing the same data with various software tools[9,10]. We demonstrate the utility of the SWATH spectral library by analyzing the zebrafish proteome in three different tissues and characterize the tissuespecific protein expression of several ohnologues
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