Backyard proteomics: A case study with the black widow spider

Abstract

Nearly all methods of mass spectrometry-based proteomics rely on knowing the proteome of the species. In less studied organisms without annotated genomes, it can seem impossible to perform proteomic analysis. In this study we sought to answer the question - does enough information exist to do proteomics on any organism we want? As a case study we started with material available due to an infestation of a home with black widow spiders. Thanks to the recent publication of an annotated genome for one species of black widow spider, we were able to identify 5502 protein groups and assign putative annotations using ortholog mapping. We also demonstrate that had we not had this resource, over 2000 proteins could be identified using other available spider genome annotations, despite their unrelatedness. Moreover, regardless of spider proteome used, proteins annotated as toxins were almost exclusively observed in the main body of the mature female black widow spider. Overall, these results provide a draft proteome map for the black widow spider and valuable data for validating machine learning models, while also suggesting that the door to insightful quantitative proteomics may already be open for millions of less studied organisms. All raw and processed proteomic data are available through the ProteomeXchange repository as accession PXD051601. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/648442v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@7e4c7eorg.highwire.dtl.DTLVardef@1cfeba1org.highwire.dtl.DTLVardef@1769a02org.highwire.dtl.DTLVardef@1790450_HPS_FORMAT_FIGEXP M_FIG C_FIG