Hi,
1) I have an mzXML file that I beleive I’ve finally correctly
converted from an ABI 5600 .wiff file. But TPP doesn't seem to like
this file. For example, when I attempt to use pep3D I get the
following error message “Empty spectrum in {insert file location}”. Is
this a file path issue (i.e. should I update file paths?) or have I
converted to mzXML incorrectly?

2) When I use the ABI file convertor tool and convert the .wiff
to .mzML, pep3D will not read this either which leads me to believe I
may need to run the update paths utility? What does this tool actually
change within the mzML/mzXML file itself?

This tool doesn't seem to work with our TPP setup so I havn't had a
chance to test it yet but am I on the right path here?

Best wishes,

Dayle

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