Skyline Spectral Libraries

Skyline Spectral Libraries wei sun2  2019-06-28

I have a question regarding how to convert DDA .wiff file from Sciex TripleTOF6600 to build Skyline Spectral Libraries.

I know ProteinPilot can do it. But do you know any other ways without ProteinPilot?

We have the biopharmaView in house.


Brendan MacLean responded:  2019-06-28

You need a Peptide Search tool. There are a lot of them out there and we are unaware of any that Skyline does not currently support. The complete list can be found here:

Some of them require converting your instrument data files (.wiff) to other formats, like Mascot General Format (MGF) or mzXML or mzML, all of which you can do with the ProteoWizard tool msconvert or MSConvertGUI (installers here:

Hope this helps. Good luck with your DDA data processing.