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Cannot open wiff file from Sciex kelvin chung  2019-07-11 00:02
 

Hello,
I am totally new in Skyline, I am trying to open the wiff file by skyline,in "import peptide search", the software prompt that the file "is not a valid library input file"

I converted the wiff file to Mzml file, and do it again, however, the same error appear ("is not a valid library input file")

are all the wiff file be the same and shall be opened by skyline ?

Thank you very much
 
 
Nick Shulman responded:  2019-07-11 06:43
The "Import Peptide Search" menu item is for importing results from a peptide search engine. Skyline does not have its own peptide search engine, but can read many peptide search result formats.

This is the list of peptide search result formats that Skyline understands:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

Do you have peptide search results in any of those formats?

If you tell us what sort of experiment you did on your mass spectrometer we will be able to point you to the tutorial that will be most helpful to you.

if you have a triple-quadrupole machine, you might want to start with the targeted method editing tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit
or if you have a full scan mass spectrometer, the place to start might be the MS1 full scan tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

-- Nick
 
kelvin chung responded:  2019-07-11 18:58
Thank you for your reply,

My sample is digested by trypsin and analyzed by Sciex 6500, for (1) peptide mapping, and (2) impurities profiling and quantitation
For impurities profiling, I have prepared the impurities sample and treated in the same way.

The SWATH workflow was followed and I got the wiff file.

what shall be the next step for using Skyline to do the analysis? thank