MSFragger with Scaffold on the command line

[Eric Kischell]

Hello,

We are integrating MSFragger with Scaffold on the command line (i.e. no Fragpipe GUI).
Does anybody know what exact files and formats (pepXML or tsv) Scaffold expects?
thx in advance
ke...@ieee.org

[Jimmy Eng]

This Scaffold help page lists supported formats including psm.tsv for Fragger:  https://support.proteomesoftware.com/hc/en-us/articles/360057031731-Scaffold-Software-Supported-Data-Formats

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