Building a spectral library from Proteome Discoverer Output

Building a spectral library from Proteome Discoverer Output r g beniston  2013-07-24 09:00
To whom it may concern (so to speak),

I'm trying to use the Mascot search results from within Proteome Discoverer 1.3/1.4 on OrbiTrap Elite generated .raw files (Nodes used are: Spectrum Files, Spectrum Selector, Mascot, Annotation and peptide validator) to build a spectral library for future use. I've exported the PSM results to a .pep.XML file and tried to build a library in Skyline v1.4 but I get the error message that the file is not from one of the recognized sources and that no spectra were found for the new library. Help, new to Skyline, and use of spectral libraries generally. Is there a get around?
Brendan MacLean responded:  2013-07-24 09:35
Hi Richard,
Skyline should be able to build a spectral library directly from a Mascot .dat file or a Proteome Discoverer .msf file. Does either of those allow you to achieve what you are looking to do?

Thanks for your interest in Skyline.

r g beniston responded:  2013-07-25 01:38
Hi Brendan,

Thanks for the quick reply. That solution sounds ideal, but under peptide settings-library tab-build library and add files I can't select the .msf file as it's not an option. If I select an .msf file through looking for any files it state an error of not being a valid library input file. AM I missing something or doing something wrong?

Best wishes.
Brendan MacLean responded:  2013-07-30 07:01
Hi Richard,
You must not have Skyline v1.4.0.4421 installed. You can check your version in the about box (Help > About). The support for MSF files was released in Skyline v1.4.0.4421. So, you will not see it in earlier releases.

You can always install the latest version manually by going to:

If you encounter problems in upgrading, then you should consult the following page:

Good luck. Thanks for using Skyline.

whwind83 responded:  2014-10-30 19:49
To whom it may concern:

I am new to Skyline and have just installed Skyline (64-bit)

I am trying to build a spectral library by importing the Proteome Discoverer 1.4 database search results .msf file into Skyline. I am using the function icon of Import DDA Peptide Search. I can add the .msf file, and the system undergoes parsing spectra, reading spectra, and filtering redundant library. However, it ends up with an empty screen showing that "spectrum information unavailable".

Did I miss anything?

Many Thanks and Warm Regards,
Wang Han
Kaipo Tamura responded:  2014-10-31 10:04
Hi Wang Han,
I have contacted you through email about this issue.

poorichaya s responded:  2024-02-01 17:21
I am a new user for skyline

I also found a problem in this issue too.

How can i fix it?


Nick Shulman responded:  2024-02-02 07:22
Can you give us more information about what you are trying to do and what is not working?
Are you seeing some sort of error message?
If you send us some files we can try to figure out what is going on.
Files which are less than 50MB can be attached to this support request.
You can upload larger files here:
-- Nick