Detecting Human Contaminant Genetically Variant Peptides in Nonhuman Samples

During proteomics data analysis, experimental spectra are searched against a user-defined protein database consisting of proteins that are reasonably expected to be present in the sample. Typically, this database contains the proteome of the organism under study concatenated with expected contaminants, such as trypsin and human keratins. However, there are additional contaminants that are not commonly added to the database. In this study, we describe a new set of protein contaminants and provide evidence that they can be detected in mass spectrometry-based proteomics data. Specifically, we provide evidence that human genetically variant peptides (GVPs) can be detected in nonhuman samples. GVPs are peptides that contain single amino acid polymorphisms that result from nonsynonymous single nucleotide polymorphisms in protein-coding regions of DNA. We reanalyzed previously collected nonhuman data-dependent acquisition (DDA) and data-independent acquisition (DIA) data sets and detected between 0 and 135 GVPs per data set. In addition, we show that GVPs are unlikely to originate from nonhuman sources and that a subset of eight GVPs are commonly detected across data sets.