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Abstract

Proteins within eukaryotic cells are organized spatially and functionally into subcellular organelles. This compartmentalization and dynamic distribution of proteins between organelles is essential for protein function and regulation of biological processes. In the genome of Pristionchus pacificus (Ppa) about one-third of genes are classified as orphans, without obvious homology in any other species, including Caenorhabditis elegans (Ce). Detailed knowledge on the subcellular distribution of Ppa proteins, will increase the use of this nematode model organism in evolutionary and molecular biology. Here, we apply an optimized method which combines biochemical cell fractionation of mixed stage worm extracts using differential ultracentrifugation and proteomics mass spectrometry, to determine the subcellular steady-state distribution of Ppa proteins. Our analysis, identified 5779 protein groups distributed among four subcellular fractions, clusters of proteins with subcellular/organelle enrichment and the first spatial resolution of multiple orphan proteins. The procedure outlined here was also applicable to study the subcellular location of Ce proteins. Our spatially resolved proteomics data will serve as an important tool to the limited resources available for studying protein biochemistry in nematodes.