TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis
TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis
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DOI：
10.1021/acs.jproteome.2c00570
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发表时间：
2023-01-11
影响因子：
4.4
通讯作者：
Petyuk, Vladislav A.
中科院分区：
文献类型：
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作者：
Martin, Evan A.;Fulcher, James M.;Petyuk, Vladislav A.
自上而下的蛋白质组学是在不进行蛋白质水解的情况下对完整形式的蛋白质进行分析，从而保留有关翻译后修饰、亚型和蛋白质水解加工的宝贵信息。然而，它仍然是一个发展中的领域，由于仪器的限制，复杂的质谱解释的困难，以及缺乏完善的定量方法。TopPIC是蛋白质组鉴定的常用工具之一。我们通过开发配套的R包（TopPICR）将其功能扩展到无标记的蛋白质定量。TopPICR管道中的关键步骤包括过滤鉴定，推断解释观察到的序列的最小蛋白质加入集，对齐保留时间，重新校准测量的质量，跨数据集聚类特征，最后使用运行间匹配方法编译特征强度。管道的输出是一个MSnSet对象，它使下游数据分析与Bioconductor项目的软件包无缝兼容。它还提供了在亲本蛋白质序列的背景下可视化蛋白质型的能力。TopPICR的功能性在10个管腔和基底乳腺肿瘤样品的人鼠异种移植物的自上而下LC-MS/MS数据集上得到证明。
Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with the interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. We extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across data sets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS data sets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.