• Sign In
  1. Requests

zenotof wiff and wiff2 data

support

View Request

view list print
zenotof wiff and wiff2 data luca nicolotti  2023-11-13 01:57
 
Hi,
I am a new user and I am struggling importing data generated using a sciex Zeno TOF, no matter what I do (convert to .mzXML, open the .wiff or the .wiff2 data) I receive this error.

---------------------------
Skyline
---------------------------
Failure opening "filename"
The file you are trying to open "filename" does not appear to be a Skyline document. Skyline documents normally have a ".sky" or ".sky.zip" filename extension and are in XML format.
---------------------------
OK More Info
---------------------------
System.IO.IOException: The file you are trying to open ( "filename"") does not appear to be a Skyline document. Skyline documents normally have a ".sky" or ".sky.zip" filename extension and are in XML format.
---------------------------

the files are all opened successfully using SciexOS
I have attached a file for reference.

Thanks for your help
 
 
Nick Shulman responded:  2023-11-13 08:01
In Skyline, the "File > Open" menu item should only be used for opening a Skyline document whose filename would usually end with ".sky".

If you want to tell Skyline to extract chromatograms from a .wiff file, the menu item that you would use is "File > Import > Results".

However, before you can use the "File > Import > Results" menu item, you need to first tell Skyline which transitions you want to monitor.

There are a lot of tutorials that can help you get started with Skyline:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials

The .wiff file that you attached looks like it was from a DDA experiment where the mass spectrometer chose the largest observed peaks for MS2 fragmentation.
If your experiment involved looking for peptides, then I might recommend that you take a look at the DDA Search for MS1 Filtering tutorial which will show you how to use the "File > Import > Peptide Search" menu item to use Skyline's built-in peptide search engine "MS Amanda" to search for peptides in a raw file and then extract MS1 chromatograms.
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search

Let us know what you were hoping to do with your .wiff file and we might be able to offer better advice.
-- Nick