1. A: Click the High Throughput Wizard icon,
    2. Set processing Options:
      1. On the Process a dataset page of the wizard, click Add and select a .raw data file. For future processing, an input file can be either a .raw file or a ProSightPC upload format (.puf ) file.
      2. In the Choose a Process Algorithm area, select a method of analysis-to-infer mass (AIM), which converts the data in the .raw data file to observed neutral mass values. Two are available: Xtract and THRASH. Both work well, although Xtract tends to be faster.
      3. In the Choose a Process Option area, select a processing option: Top Down (MS2), Top Down (MS3), or Middle Down or manually set the parameters (Advanced Settings).
      4. Click Next.
    3. Prepare Repository and Search Tree
      1. Select an existing repository from the Repository list or create a new repository.
        1. Click New Repository.
        2. Give your repository a name.
        3. ProSightPC provides two default categories, “good” and “bad,” when creating a new repository.
        4. Click Save.
      2. Select an existing search tree from the Search Tree List or create a new search tree
      3. A search tree can hold one or more branch points. Each branch point in the tree contains one search. The simplest search tree has one branch point; this is the default for a new tree. You can create a new search or select an existing search.
        1. If you want to select an existing search and are running the example files, select Demo Search Tree from the Search Tree Name list.
        2. To create a new search tree
          1. To create a search, click Add Search.
          2. (Optional) Add a predefined search or edit an existing predefined search.
          3. Click Save.
          4. Select a predefined search or create a new search.
          5. To select a condition, click Conditions.
          6. Set conditions that determine if the experiment will be loaded to the “good” category representing high-quality data or to the “bad” category representing low-quality data. The default of E-value < 1e-4 filters confident hits.
          7. (Optional) Specify a two-level search tree by changing load to run search, and repeat this process.
        3. (Optional) Select the options in the Experiment Filter box to ignore experiments that are not likely to yield matches. By default, these are:
          1. Experiments that contain less than 10 fragments
          2. Experiments whose intact mass is less than 750 Da
        4. Click Save.
      4. Run HighThroughput Mode!
        1. Review your settings in the Summary window.
        2. To begin the ProSightPC High Throughput processing, select Process at the bottom.
        3. When the High Throughput wizard finishes processing the data, click Finish.
    Answered by Webmaster ears ago
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