Data for 'PSMatch: an R/Bioconductor package to explore proteomics identification data.'

This archive stores the files used for the demonstration of the PSMatch package. The mzML file contains the observed spectra and was downloaded from the PRIDE repository PXD039419 . The .tsv file contains the identification data (PSMs) and was generated by the search engine Sage v.0.14.6. The .json file contains the search engine parameters that were used to generate the PSMs. We present the R/Bioconductor PSMatch package, that helps proteomics practitioners to load, manage and handle peptide spectrum matches. It provides functions to model peptide-protein relations, visualise these as graphs and make informed decisions about shared peptide filtering. The package also provides functions to calculate and, in conjunction with the Spectra package, annotate and visualise MS2 scans.本归档文件存储了用于演示PSMatch软件包（PSMatch）的相关文件。 该mzML格式文件收录了实测质谱谱图，其下载自PRIDE数据库PXD039419。 该.tsv格式文件包含肽段谱匹配（Peptide Spectrum Matches，PSMs）鉴定数据，由搜索引擎Sage v.0.14.6生成。 该.json格式文件包含用于生成肽段谱匹配的搜索引擎配置参数。 本文介绍了R/Bioconductor生态下的PSMatch软件包（PSMatch），可助力蛋白质组学研究者完成肽段谱匹配数据的加载、管理与处理。该软件包提供了肽段-蛋白关联关系建模函数，支持将此类关系以图谱形式可视化，并可为共享肽段的过滤工作提供科学决策支撑。此外，该软件包还具备计算功能，可结合Spectra软件包对MS2质谱扫描图进行注释与可视化。