RATIONALE A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS infrastructure. METHODS An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra. RESULTS Data acquisition and processing required ~2 h and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST. CONCLUSIONS MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

中文翻译：

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全球自然产品社交分子网络基础架构中社区创建的公共MS / MS参考光谱的协议。

理由在质谱实验中鉴定化学品的主要障碍是公共数据库中串联质谱（MS / MS）参考光谱的可用性。当前，科学家购买数据库或使用公共数据库，例如全球天然产物社会分子网络（GNPS）。MSMS-Chooser工作流是一个开源协议，用于直接在GNPS基础结构中创建MS / MS参考光谱。方法提供并手动完成了MSMS-Chooser示例模板。MSMS-Chooser提交文件和用于数据采集的序列表以编程方式生成。分析了悬浮在甲醇-水（1：1）溶液中的质谱代谢物库（MSMLS）的标准品。使用LC / MS / MS系统上的流动注射使用依赖于数据的采集来生成负模和正模数据。MS / MS光谱和提交文件已上载到GNPS中的MSMS-Chooser工作流程中，用于自动选择MS / MS光谱。结果使用MSMS-Chooser，每个96孔板分别需要约2 h和〜2 min进行数据采集和处理。使用MSMS-Chooser对600多个小分子进行的MSMLS分析为GNPS的公共图书馆增加了889个光谱（包括多个加合物）。手动验证一块板表明可以正确选择MS / MS扫描（真实阳性率为0.96，真实阴性率为0.99）。MSMS-Chooser输出包括格式化为包含在GNPS库中的表以及通过MASST直接启动搜索的功能。结论MSMS-Chooser可实现快速数据采集，数据分析（选择MS / MS光谱），以及用于检查并上传到GNPS的格式化表格。可以使用MSMS-Chooser处理来自大多数包含MS / MS质谱图的质谱平台的打开文件格式数据（.mzML或.mzXML）。MSMS-Chooser使GNPS中MS / MS参考光谱的创建民主化，这将改善注释并增强使用注释信息的工具。