With the Metabolomics App in the OneOmics suite, it is possible to upload a custom ion library for peak extraction by the Extractor App during the processing of SWATH acquisition data. When creating an ion library for use in the Metabolomics app, be sure to create a separate ion library for use with samples acquired in positive polarity and negative polarity, and to use fragment ions from consensus spectral data, which should be in the form of a peak list.

The custom ion library must be a text (.txt) file with tab-separated columns. Table 1 summarizes the specific requirements for the text file when creating a custom ion library for the Metabolomics app, and Figure 1 is a screenshot of an example text file library displayed in a spreadsheet format. Note that the order of the column headers in the text file does not matter, and the names of the columns are case-insensitive. The overall format of the text file is based on SWATH acquisition proteomics libraries, with proteomics-based terms used for the column headers. The optional ce column is for information purposes only, meaning that it is not used to influence the selection of fragment ions or compounds by the Extractor app. Similarly, the rt_detected column is not used to influence the extracted ion chromatogram (XIC) peak finding range.

Table 1. A custom ion library for metabolomics data processing must be a text file with a specific set of tab-separated columns. While the inclusion of certain columns is mandatory, the order of the columns in the file does not matter and the names are case-insensitive.

Figure 1. In this example, the contents of the custom ion library text file are displayed in a spreadsheet format.

Once the text file is formatted, it can be uploaded to the cloud using CloudConnect in PeakView software 2.2. It can then be selected for processing by the Extractor app using the ADD/REMOVE FILES button in the Custom Ion Library Files section of the Extractor app settings (Figure 2). Note that ion library merging is not supported in the Extractor app, so only 1 library file can be used for a specific processing job. Once the file has been added, its name will appear in the Extractor App settings window, which means it is ready to be used in data processing.

Figure 2. Add the custom library file to make it available for processing in the Extractor app.

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