Support for Skyline-built spectral libraries in DIALib-QC tool

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Jakub Červenka

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Oct 21, 2022, 10:28:03 AM10/21/22
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Dear all,

 I would like to use your DIALib-QC tool for spectral libraries that were built in Skyline. I tried to export library from Skyline in format for Spectronaut (Skyline Schema for exporting Spectronaut compatible libraries - https://biognosys.com/resources/spectronaut-further-user-resources/) and used this file for DIALib-QC tool (http://www.swathatlas.org/DIALibQC.php), but I was not able to get any results. In fact, have got only an empty web page (see attachment).

 Is there any way how to analyze spectral libraries from Skyline? I contacted Skyline support for help, but we were not successful with running DIALib-QC tool (https://skyline.ms/announcements/home/support/thread.view?rowId=57092).

 Would be possible to add the Skyline type of spectral libraries to supported formats for DIALib-QC tool? I am sure that many Skyline users would appreciate it.

 Thank you very much!

 

Jakub

 

Charu Midha

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Oct 21, 2022, 12:10:22 PM10/21/22
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Hi Jakub, 

Thankyou for using DIALib-QC for assessing your skyline library. For libraries more than 200MB, you need to download and install the DIALibQC tool locally to your machine for its assessment. What is your library size?
Also can you please share a demo tiny version of your skyline library for me to look at?

Best, 
Charu
 

Charu K Midha, PhD,

Post Doc Fellow

Moritz's Lab, ISB,




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Jakub Červenka

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Oct 31, 2022, 9:57:40 AM10/31/22
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Hi Charu,

Thank you very much for your reply! I am sorry for such a long delay in responding, but I was out of my office.

I am a little bit confused – does DIALib-QC support spectral libraries from Skyline? I tried to assess several ion libraries via web-interface at https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/AssessDIALibrary, both in Skyline format (non-redundant .blib file) as well as in Spectronaut format export from Skyline (.csv and .txt). Unfortunately, I was not successful as after analysis – no data were shown. I have not tried a desktop version yet.

My libraries have different sizes, but non-redundant libraries are below 200 MB (typically between 10 and 120 MB), redundant libraries are over 100 MB up to 500 MB. So I hope that it should not be the issue in case of non-redundant library.

Thank you very much, I would appreciate the possibility to send you a demo version of one of my libraries. Should I share it here or directly or should I use a sharing service (e.g. WeTransfer)?

Thank you once again!

Best wishes,

Jakub

Dne pátek 21. října 2022 v 18:10:22 UTC+2 uživatel cmi...@systemsbiology.org napsal:

Charu Midha

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Oct 31, 2022, 11:32:17 AM10/31/22
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Hi Jakub, 

DIALib-QC currently supports assessing spectronaut/peakview/openswath/prosite (exported in spectronaut format) libraries and not the .blib format. Can you please share the demo or non-redundant library of ~10MB  in spectronaut format (both .txt and .csv) exported from skyline directly to me? I can check what is going on and troubleshoot.

Best
Charu

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