Detecting genetically variant peptides in non-human samples

Abstract

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 are detectable in mass spectrometry-based proteomics data. Specifically, we provide evidence that human genetically variant peptides (GVPs) can be detected in non-human samples. GVPs are peptides that contain single amino acid polymorphisms that result from non-synonymous single nucleotide polymorphisms in protein coding regions of DNA. We reanalyzed previously collected non-human data-dependent acquisition (DDA) and data-independent acquisition (DIA) datasets and detected between 0 and 135 GVPs per dataset. In addition, we show that GVPs are unlikely to originate from non-human sources and that a subset of eight GVPs are commonly detected across datasets.