How to input the .sptxt file

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How to input the .sptxt file sunrui  2018-12-30
 

what is the format of the skyline, which column is the necessary for the skyline to recognize. I input the sptxt file, however there is a error that the sptxt file is not a valid file. if someone know the answer, please tell me.

 
 
Brendan MacLean responded:  2018-12-30

Hi Sun Rui,
You can add the .sptxt file to Skyline directly as a spectral library by doing the following:

  • Settings > Peptide Settings - Library tab
  • Click the Edit List button
  • Click the Add button
  • Give the library a name
  • Click the Browse button - and choose your .sptxt file
  • Click OK to add the library
  • Click OK to close Edit List
  • Make sure your new library is checked
  • Click OK to close the Peptide Settings form

Once you have added the library, how you use it will depend on your intended experiment. If you will choose a limited, targeted subset of the peptides in your library for a method like SRM/MRM or PRM, then the best place to start would be doing the Targeted Method Editing tutorial:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit

Which has been translated to Chinese:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit_zh

If you will be analyzing DDA data, then you should also look at the MS1 Full-Scan Filtering tutorial:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

Again translated to Chinese:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering_zh

If you will be analyzing DIA data, then I would recommend the ETH tutorial on DIA analysis with Skyline:

http://dia-swath-course.ethz.ch/downloads.html

Which we recently translated to Chinese for the Shanghai course:

https://skyline.ms/project/home/software/Skyline/events/2018 Shanghai Course/participants/begin.view

You can find it in the "ETH" subfolder on this page.

Hope this helps. Thanks for making the effort to begin using Skyline in your research.

--Brendan