SkylineRunner: Input a FASTA file and Output an Isolation List

SkylineRunner: Input a FASTA file and Output an Isolation List michael creech  2016-04-18
We are trying to use SkylineRunner (v3.5) to obtain an isolation list given a list of proteins in FASTA format. To make this completely clear, we want to do the same thing as the following set of Skyline operations:

    1)Start Skyline, input (attached) [this is an empty .sky file with a few settings in it]
    2)Perform File->Import->FASTA… pAMP-Input-4-14.fasta (attached)
    3)Perform File->Export->Isolation List…, use default settings and click OK, then choose file name, such as test.csv

This works fine in Skyline, but when we attempt this using SkylineRunner, we run into two problems:

    A)SkylineRunner claims to go thru all the motions of performing the above steps, but never writes out the test.csv file.
    B)We can’t figure out how to specify an isolation list (we did see that we can do a transition list, and tried that for the experiment below).

We are running on Windows 7, with version 3.5. Here’s an example of what we have tried using SkylineRunner, and the above mentioned files:

    C:\work\AMP\AMP\target\test-classes\HeLa-Targeted>skylinerunner.exe --import-fasta=pAMP-Input-4-14.fasta --exp-strategy=single --exp-translist-instrument=Agilent --exp-file=test.csv
    Opening file...
    File opened.
    Importing FASTA file pAMP-Input-4-14.fasta...
    List test.csv exported successfully.

Note that we also checked to make sure the test.csv file wasn’t being written to some other, unexpected place. We did this by simply replacing the file with another non-empty .sky file and the test.csv file appeared.
Kaipo responded:  2016-04-19
I believe that the first issue you are having is a bug that was resolved after the 3.5 release. Can you retry it with Skyline-daily?
I was able to run your command and generate a valid csv file.

For the second issue, it is not yet supported to export isolation lists from SkylineRunner but I have created an issue in our issue tracker to add this.

michael creech responded:  2016-04-19
Great! That's certainly a start--I can now generate transition lists. Now if we can just get isolation lists, we will be in business!

One minor issue I ran into in where to place the background proteome file and spectral library. Are there any SkylineRunner parameter options to control where it searches for these?
Kaipo responded:  2016-04-20
For background proteome, it is not currently possible - it would need to be set up in your Skyline input template file before calling SkylineRunner.
For spectral libraries, it should be possible to add one to the document with --add-library-path=path/to/file, but not changing the path of a library that already exists within the document.

alex apffel responded:  2016-04-20
Hi Kaipo,
For our workflow, generating isolation lists will be pretty critical. With respect to Skyline Runner feature requests and revisions, can you give us an idea of how responsive you are and what the time frame is? If it's quick. We'll plan for that, if not, we may try to extract data from a transition list.
Kaipo responded:  2016-04-20
Hi Alex,
I expect that it will be pretty straightforward to implement, so I will work on adding it and hopefully it will make it into the next Skyline-daily release.

michael creech responded:  2016-04-21
That would be awesome!!
Kaipo responded:  2016-04-21
This option will be available in the next release of Skyline-daily as --exp-isolationlist-instrument=...

michael creech responded:  2016-04-22
How often is "daily" version generated? I checked this morning, but it seems to be the same version number as it did a few days ago (e.g., and doesn't contain the change.
michael creech responded:  2016-04-30
I've just tried SkylineDaily version and it still doesn't recognize the isolationlist argument:

     Stdout: Error: Unexpected argument --exp-isolationlist-instrument

Is the isolation list update missing in 9489, or is this a bug?
Kaipo responded:  2016-05-02
Hi Michael,
Sorry - a new Skyline-daily has not been released since the option was added. You can see the Skyline-daily releases here:
The update should be released soon.

YangZhang responded:  2016-08-31
Any update on this? It would be a super nice feature to have.
Brian Pratt responded:  2016-08-31
This should be enabled in the current Skyline-Daily release, I believe.

YangZhang responded:  2016-08-31
Sorry, I should try first, it is indeed working! I just searched release notes and the manual for skylinedailyrunner and it was not there yet, Thanks a lot!
Brendan MacLean responded:  2016-08-31
There is mention of it being added in the release notes for Skyline-daily v3.5.1.9673, which was the release just after mentioned by Michael Creech:

But, you were right about the documentation not having been updated. Happily this was just a matter of updating the PDF on the website as the code changes were reflected in the documentation committed to the project source repository. This also adds documentation for new options that can be used to add decoys for people seeking to automate DIA data processing with mProphet peak picking.

Thanks for checking on this.

YangZhang responded:  2016-08-31
Thanks again!