mpwR：一个用于比较基于质谱的蛋白质组学工作流程性能的 R 包。
mpwR: an R package for comparing performance of mass spectrometry-based proteomic workflows.
机构信息
Metabolomics and Proteomics Core (MPC), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 80939 München, Germany.
German Center for Neurodegenerative Diseases (DZNE) Munich, DZNE, 81377 München, Germany.
出版信息
Bioinformatics. 2023 Jun 1;39(6). doi: 10.1093/bioinformatics/btad358.
SUMMARY
mpwR is an R package for a standardized comparison of mass spectrometry (MS)-based proteomic label-free workflows recorded by data-dependent or data-independent spectral acquisition. The user-friendly design allows easy access to compare the influence of sample preparation procedures, combinations of liquid chromatography (LC)-MS setups, as well as intra- and inter-software differences on critical performance measures across an unlimited number of analyses. mpwR supports outputs of commonly used software for bottom-up proteomics, such as ProteomeDiscoverer, Spectronaut, MaxQuant, and DIA-NN.
AVAILABILITY AND IMPLEMENTATION
mpwR is available as an open-source R package. Release versions can be accessed on CRAN (https://CRAN.R-project.org/package=mpwR) for all major operating systems. The development version is maintained on GitHub (https://github.com/okdll/mpwR) and full documentation with examples and workflow templates is provided via the package website (https://okdll.github.io/mpwR/).
摘要
mpwR 是一个 R 包，用于标准化比较基于质谱（MS）的蛋白质组学无标记工作流程，这些工作流程由数据依赖或数据独立的光谱采集记录。用户友好的设计允许轻松访问，以比较样品制备程序、液相色谱（LC）-MS 设定组合以及内在和软件之间的差异对跨无限数量分析的关键性能指标的影响。mpwR 支持常用的用于自上而下蛋白质组学的软件的输出，如 ProteomeDiscoverer、Spectronaut、MaxQuant 和 DIA-NN。
可用性和实现
mpwR 作为一个开源 R 包提供。所有主要操作系统均可在 CRAN（https://CRAN.R-project.org/package=mpwR）上访问发行版本。开发版本在 GitHub（https://github.com/okdll/mpwR）上维护，并通过包网站（https://okdll.github.io/mpwR/）提供完整的文档，包括示例和工作流程模板。
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