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J Proteome Res. 2014 Mar 7;13(3):1537-44. doi: 10.1021/pr4010585. Epub 2014 Feb 5.

Identifying proteins in zebrafish embryos using spectral libraries generated from dissected adult organs and tissues.

Author information

1
Center for Proteomics and Metabolomics, Leiden University Medical Center , Albinusdreef 2, Leiden 2300 RC, The Netherlands.

Abstract

Spectral libraries provide a sensitive and accurate method for identifying peptides from tandem mass spectra, complementary to searching genome-derived databases or sequencing de novo. Their application requires comprehensive libraries including peptides from low-abundant proteins. Here we describe a method for constructing such libraries using biological differentiation to "fractionate" the proteome by harvesting adult organs and tissues and build comprehensive libraries for identifying proteins in zebrafish (Danio rerio) embryos and larvae (an important and widely used model system). Hierarchical clustering using direct comparison of spectra was used to prioritize organ selection. The resulting and publicly available library covers 14,164 proteins, significantly improved the number of peptide-spectrum matches in zebrafish developmental stages, and can be used on data from different instruments and laboratories. The library contains information on tissue and organ expression of these proteins and is also applicable for adult experiments. The approach itself is not limited to zebrafish but would work for any model system.

PMID:
24460240
DOI:
10.1021/pr4010585
[Indexed for MEDLINE]

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