SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
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DOI：
10.1371/journal.pone.0153160
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Aebersold R
中科院分区：
文献类型：
--
作者：
Blattmann P;Heusel M;Aebersold R
SWATH-MS是一种靶向蛋白质组学的采集和分析技术，能够在许多样品中以高再现性和准确性测量数千种蛋白质。OpenSWATH是一个流行的开源软件，用于从SWATH-MS数据中进行肽鉴定和定量。对于下游的统计和定量分析，有不同的工具，如MSstats， mapDIA和aLFQ。然而，将数据从OpenSWATH传输到下游统计工具目前在技术上具有挑战性。在这里，我们介绍R/Bioconductor软件包SWATH2stats，它可以方便地将数据处理成下游分析工具可直接读取的格式。此外，SWATH2stats允许注释、分析测量的变化和再现性、FDR估计以及在将处理后的数据提交给下游工具之前进行高级过滤。这些功能对于快速分析SWATH-MS数据质量非常重要。因此，SWATH2stats是一个新的开源工具，它总结了分析、处理和转换SWATH- ms数据的几个实用功能，从而促进了大规模SWATH/DIA数据集的有效分析。
SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.