Detecting Human Contaminant Genetically Variant Peptides in Nonhuman Samples.

IF 3.8 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Fanny Chu, Andy Lin
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引用次数: 0

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 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.

在蛋白质组学数据分析过程中,实验光谱会根据用户定义的蛋白质数据库进行搜索,该数据库由可合理预期存在于样本中的蛋白质组成。通常情况下,该数据库包含所研究生物的蛋白质组和预期的污染物,如胰蛋白酶和人类角蛋白。然而,还有一些额外的污染物并没有被添加到数据库中。在本研究中,我们描述了一组新的蛋白质污染物,并提供证据证明它们可以在基于质谱的蛋白质组学数据中被检测到。具体来说,我们提供了在非人类样本中可以检测到人类基因变异肽(GVPs)的证据。GVPs 是含有单氨基酸多态性的肽,这些多态性由 DNA 蛋白编码区的非同义单核苷酸多态性引起。我们重新分析了以前收集的非人类数据依赖性采集(DDA)和数据非依赖性采集(DIA)数据集,每个数据集检测到 0 到 135 个 GVP。此外,我们还发现,GVPs 不太可能来自非人类,而且在各数据集中普遍检测到 8 个 GVPs 子集。
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来源期刊
Journal of Proteome Research
Journal of Proteome Research 生物-生化研究方法
CiteScore
9.00
自引率
4.50%
发文量
251
审稿时长
3 months
期刊介绍: Journal of Proteome Research publishes content encompassing all aspects of global protein analysis and function, including the dynamic aspects of genomics, spatio-temporal proteomics, metabonomics and metabolomics, clinical and agricultural proteomics, as well as advances in methodology including bioinformatics. The theme and emphasis is on a multidisciplinary approach to the life sciences through the synergy between the different types of "omics".
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