Different types of skyline files

Different types of skyline files heyang  2020-02-27 07:03

Hi Skyline team,

Just want to know details about different types of skyline files, e.g document, view, skyl and chromatogram data. if I want to upload a result to panarama, I need to upload all 4 files, or just document file. thanks,


Brendan MacLean responded:  2020-02-27 07:20

Hi Heyi,
I just answered a separate support request (posted after yours) about what the .skyl file is here:


Generally, we don't recommend trying to send these files by themselves for the purpose of sharing a Skyline document/project. Instead you should either use: 1) File > Share, 2) File > Upload to Panorama. Both will package everything necessary into a ZIP file. I also use File > Share to make a handy snapshot of the entire project at a certain state. The ZIP file contains everything, including spectral and iRT libraries and when you then open it with File > Open the files are extracted into a separate folder, which you can do any number of times, allowing you to start from the same snapshot over and over.

Hope this helps. Thanks for posting your question to the Skyline support board.


Brendan MacLean responded:  2020-02-27 07:35

Here is a complete (I hope) list of Skyline file types:

  • .sky - the main Skyline document file
  • .sky.view - contains state information about the Skyline UI when the .sky file was last saved, e.g. selection and window layout - can be deleted
  • .skyd - contains all the chromatograms and the complete set of peak statistics (generally 10 per chromatogram) considered by Skyline
  • .skyl - the Skyline audit log file
  • .blib - a Skyline native spectral library
  • .slc - a "spectral library cache" created to improve initial spectral library load performance - can be deleted and Skyline will simply recreate it
  • .irtdb - a Skyline iRT library file
  • .optdb - a Skyline optimization library for CE and CoV optimization values
  • .protdb - a background proteome file
  • .imsdb - and ion mobility library (coming in 20.2) which stores ion mobility and CCS values

External library types:

  • .hlf - X! Hunter spectral library from theGPM
  • .sptxt - SpectraST spectral library from the TPP
  • .msp - NIST spectral library

But don't try to understand all of the above just to share a complete Skyline document/project with others, instead use File > Share or Upload to Panorama to create a:

  • .sky.zip - a compressed ZIP archive which contains the full set of files required to share your document/project

Exported files not associated with the .sky file:

  • .skys - a Skyline settings file which can be imported into a menu item on the Skyline Settings menu
  • .skyr - a Skyline report template file which can be imported back into Skyline to add report templates to the available set
  • .skyp - a new Skyline "pointer" file that can be downloaded from Panorama very quickly and will then initiate a full download inside Skyline when opened
heyang responded:  2020-02-27 08:19

Thank you, Brendan! So helpful,

Vagisha Sharma responded:  2020-02-27 09:00

Hi Heyi,

If needed, you can also refer to this documentation on uploading Skyline documents to Panorama: https://panoramaweb.org/doc_import_into_panorama.url


roman sakson responded:  2021-07-22 12:35

Hi everyone,

Vagisha kindly referred me to that post because of some other issue I had. The list is very helpful! Just for the sake of completeness, I believe that the .midas file ending for specialized Sciex files is missing in the above list.

Big thanks to Brendan, Vagisha and everyone involved for their continuous support!

Brendan MacLean responded:  2021-07-23 10:28

I have created a new Tip page with this information on it and the .midas file type added. Thanks for your feedback, Roman.