Shotgun proteomics is a very sensitive bottom-up approach used to study complex mixtures of proteins through a combination of high-performance liquid chromatography (HPLC) and high-resolution mass spectrometry (HRMS). This technique has been successfully applied to the study of olfactory appendixes of insects and other arthropods. Since extracting soluble proteins from tissues and processing them for shotgun proteomics is quite straightforward, the technique has proved to be very suitable for studying soluble olfactory proteins, such as odorant binding proteins (OBPs), chemosensory proteins (CSPs) and Niemann-Pick type 2 proteins. Here, we describe the main principles and methods at the basis of shotgun proteomics, including its use to quantify proteins through label-free quantification. We also provide operational protocols for the experimental workflow steps, i.e., insect dissection, protein extraction, protein enzymatic digestion, sample purification, HPLC-MS analysis, search of mass spectral data against polypeptide databases and first steps in the analysis of the search results.
Keywords: CPSs; Insect antennae; NPC2 proteins; OBPs; Shotgun proteomics.
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