Institute for Systems Biology, Seattle, Washington 98109, United States.
J Proteome Res. 2021 Apr 2;20(4):1911-1917. doi: 10.1021/acs.jproteome.0c00928. Epub 2021 Feb 2.
The efficiency of shotgun proteomic analysis is dependent on the reproducibility of the peptide cleavage process during sample preparation. To generate rapid and useful metrics for peptide cleavage efficiency, as in enzymatic or chemical cleavage, SPACEPro was developed to evaluate efficiency and reproducibility of protein cleavage in peptide samples following data-dependent analysis by mass spectrometry. SPACEPro analyzes samples at the peptide-spectrum match (PSM), peptide, and protein levels to provide a comprehensive representation of the overall sample processing to peptides. All output is provided in human-readable text and JSON files that can be further processed to assess the cleavage efficiency on proteins within the sample. SPACEPro provides a snapshot of the protein cleavage efficiency through very minimal effort so that the user is informed of the quality of the sample processing efficiency and can accordingly develop protocols to improve the initial sample preparation for subsequent analyses.
Shotgun 蛋白质组学分析的效率取决于样品制备过程中肽裂解过程的重现性。为了生成类似于酶切或化学裂解的肽裂解效率的快速且有用的指标，开发了 SPACEPro 来评估肽样品中蛋白质裂解的效率和重现性，该方法通过质谱进行数据依赖分析。SPACEPro 在肽谱匹配（PSM）、肽和蛋白质水平上分析样品，以提供对整个样品处理到肽的综合表示。所有输出都以人类可读的文本和 JSON 文件提供，可进一步处理以评估样品中蛋白质的裂解效率。SPACEPro 通过非常少的努力提供了蛋白质裂解效率的快照，使用户了解样品处理效率的质量，并可以相应地制定协议来改进初始样品准备，以进行后续分析。
