mzXML Format File:

At present, the MS2 batch search accepts only mzXML files as input; here is an example.
Thermo RAW files can be converted to mzXML format using RawConverter.
Other types of MS/MS data can be converted to mzXML format using pwiz-setup-3.0.

Single Work Pipelines:

On the batch search page, you can choose between two pipelines: Single Work and Group Work. In Single Work mode, raw data are annotated one sample at a time, as shown below.

Once a sample (in mzXML format) has been uploaded, click Run Query to upload and match it; an uploaded file will appear in the list as shown below. The sample list displays each sample's type, file name, file size, RT range, polarity, scan count, upload status, parsing status, and match status.

Click the icon in the Parsing Status column to view the chromatogram details, as shown below.

Click Match in the action bar to compare the sample against the database and obtain the annotation results, then click Show Hits to view them, as shown below. Each search result includes query peak, matched compound info, matched spectrum info, and matched peak info.

Clicking a link in a result field opens the detailed page or an enlarged view of the corresponding content — for example, Peak ID, MS/MS ID, and Match Peaks.

Clicking a compound ID opens the compound's detailed page at NCBI.

Group Work Pipelines:

In Group Work mode, select at least two sample files, then click Upload to upload the raw data to the nodes.

As in Single Work mode, sample details are shown in the sample list, and upload and parsing progress is updated in real time.

After all samples are uploaded, click Run Adjust to select reference samples and run Group Alignment to adjust RT, as shown below.

Click the circled button below to view a chromatogram of the currently uploaded sample set.

Click the circled button below to view the query results for this sample set.

Finally, click Run Query to start the matching process; the progress is shown in the table below.

Once matching is complete, click the button shown below to view query peak, matched spectrum info, compound info, and sample intensity. As in Single Work mode, you can also click links in the results to access the corresponding details.

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