Chang Hui-Yin, Kong Andy T, da Veiga Leprevost Felipe, Avtonomov Dmitry M, Haynes Sarah E, Nesvizhskii Alexey I
Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States.
J Proteome Res. 2020 Jun 5;19(6):2511-2515. doi: 10.1021/acs.jproteome.0c00119. Epub 2020 May 8.
Shotgun proteomics using liquid chromatography coupled to mass spectrometry (LC-MS) is commonly used to identify peptides containing post-translational modifications. With the emergence of fast database search tools such as MSFragger, the approach of enlarging precursor mass tolerances during the search (termed "open search") has been increasingly used for comprehensive characterization of post-translational and chemical modifications of protein samples. However, not all mass shifts detected using the open search strategy represent true modifications, as artifacts exist from sources such as unaccounted missed cleavages or peptide co-fragmentation (chimeric MS/MS spectra). Here, we present Crystal-C, a computational tool that detects and removes such artifacts from open search results. Our analysis using Crystal-C shows that, in a typical shotgun proteomics data set, the number of such observations is relatively small. Nevertheless, removing these artifacts helps to simplify the interpretation of the mass shift histograms, which in turn should improve the ability of open search-based tools to detect potentially interesting mass shifts for follow-up investigation.
使用液相色谱-质谱联用（LC-MS）的鸟枪法蛋白质组学常用于鉴定含有翻译后修饰的肽段。随着诸如MSFragger等快速数据库搜索工具的出现，在搜索过程中扩大前体质量容差的方法（称为“开放式搜索”）越来越多地用于全面表征蛋白质样品的翻译后修饰和化学修饰。然而，并非所有使用开放式搜索策略检测到的质量偏移都代表真正的修饰，因为存在诸如未考虑的酶切缺失或肽段共碎裂（嵌合MS/MS谱图）等来源产生的假象。在此，我们介绍Crystal-C，一种从开放式搜索结果中检测并去除此类假象的计算工具。我们使用Crystal-C进行的分析表明，在典型的鸟枪法蛋白质组学数据集中，此类观测结果的数量相对较少。尽管如此，去除这些假象有助于简化质量偏移直方图的解读，进而应能提高基于开放式搜索的工具检测潜在有趣质量偏移以供后续研究的能力。
