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The complexity in chemical composition alongside the genomic complexity of crop plants poses significant challenges for the characterization of their proteomes. This chapter provides specific methods that can be used for the extraction and identification of proteins from sweet potato, and a proteogenomic method for the subsequent peptide mapping on the haplotype-derived sweet potato genome assembly. We outline two basic methods for extracting proteins expressed in root and leaf tissues for the label-free quantitative proteomics—one phenol-based procedure and one polyethylene glycol (PEG) 4000-based fractionation method—and discuss strategies for the organ-specific protein extraction and increased recovery of low-abundance proteins. Next, we describe computational methods for improved proteome annotation of sweet potato based on aggregated genomics and transcriptomics resources available in …