impossible to read wiff2 files

impossible to read wiff2 files nicolas drouin  2021-05-27

Dear Skyline team,

i remembered a newsletter indicating the wiff2 from Sciex can now be read with skyline.
However, I'am encountering difficulties to do so. Only solution i found is to convert the wiff2 in mzml using MS convert, but for some reasons, i have to convert the data one by one for the conversion fails (not all the chromatogram is converted in batch mode :( )
I have proteomic data from a X500r QTOF running SciexOS (version

Please find enclosed one of my file containing full scan data of a BSA digest.

Many thanks in advance for your help.

Nick Shulman responded:  2021-05-27

It sounds like you were planning on attaching some files to this support request, but not files have been attached.
Sometimes this happens if your files are too large. The maximum size for files attached to a support request is 50MB.
You can upload larger files here:

Currently, the only .wiff2 files that Skyline and MSConvert can read are from the x500 machine, and it sounds like that is the type of machine that you have.

In general, any file that MSConvert can read Skyline is also supposed to be able to read, so you should not have to do the conversion to mzML.

It sounds like a number of things are going wrong. Please send us your files and we will investigate why Skyline is having trouble with your wiff2 files, and why MSConvert is giving you different results depending on whether you convert a single or multiple files.
-- Nick