Searching with MSFragger and X! Tandem in Scaffold 5

Can I search data using MSFragger and X! Tandem at the same time?

Scaffold 5 introduced the ability to search data using MSFragger. This can be used to search either raw data or as a confirmatory search when search engine results are loaded.

Scaffold can do X! Tandem full searches. Scaffold can also use X! Tandem as a confirmatory search engine but only when search engine results are loaded. You have to go to Edit > Preferences > Paths and set up your X! Tandem executable and choose it with the radio button. X! Tandem doesn't search from raw files. It needs a peaklist, like mzML, MGF, DTA or PKL.

You cannot search data using both MSFragger and X! Tandem whether it is raw data or data from an existing search.

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