the conversion of spectronaut library in EncyclopeDIA

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the conversion of spectronaut library in EncyclopeDIA sunbergsoon  2019-11-26
 

Hi,

recently I tried the EncyclopeDIA from your group, I want to use the library built by spectronaut.
However, I got nothing after conversion. So could you give me some advice about the format
and details on this ?

Thanks a lot.

Sunberg

 
 
sunbergsoon responded:  2019-11-28

or where and who I contact to solve the problem?

thanks a lot.

Sunberg

 
Brendan MacLean responded:  2019-11-28

Hi Sunberg,
I believe EncyclopeDIA accepts a .blib file. So, you could try File > Import > Assay Library to go from Spectronaut into Skyline. If you can get that to work, which it should in many cases, if you use a CSV from Spectronaut, this will cause Skyline to produce a .blib file, and you likely can use that .blib file with EncyclopeDIA. Though, EncyclopeDIA may work best with more fully expressed MS/MS spectra. e.g. Spectronaut may have reduced them to just 6 peaks.

You might want to try backing up a step to building the library inside Skyline, which you definitely can also use in Spectronaut. I have seen that Biognosys provides a Skyline report template for transferring a library from Skyline to Spectronaut.

If you use Skyline to build the library from DDA results, then you could use that .blib in EncyclopeDIA. If you have used Spectronaut to build your library directly from DIA data, however, then you are likely back to trying to get that into Skyline with File > Import > Assay Library and using the resulting .blib with EncyclopeDIA. I would just try to get as complete a set of fragment ions peaks as you can out of Spectronaut.

Hope this helps.

--Brendan

 
sunbergsoon responded:  2019-11-28

Hi Brendan,
Thanks so much for your kind reply and help!
For now I just get stuck on the conversion library built by spectronaut in EncyclopeDIA: Convert > Convert Prosit/Spectronaut CSV to Library.
I tried several file format, and got nothing after conversion.

I attached some format and specific columns in .txt format which I tried with .csv in EncyclopeDIA.

Could you please give me some advices on the format of the .csv library?

Thanks a lot.

Best regards,
Sunberg

 
Brendan MacLean responded:  2019-11-28

Hi Sunberg,
This is really beyond the support I could hope to give you on EncyclopeDIA, which is really the work of Brian Searle, who has left our lab for a post doc at the ISB. I have forwarded your request to Brian and I hope he will soon either give me an alternate EncyclopeDIA support web page or take up this thread soon. However, it is a long holiday weekend in the U.S. So, I wouldn't be at all surprised if you had to wait until Monday, December 2 for a response.

--Brendan

 
sunbergsoon responded:  2019-11-28

Hi Brendan,

Thanks quite a lot, hopefully we could get the solution ASAP.

Thanks a lot!

Sunberg

 
Brendan MacLean responded:  2019-11-28

Word from Brian: "I've made the issue tracker public: https://bitbucket.org/searleb/encyclopedia/issues"

Give that a shot and see if Brian can help you with this.

 
sunbergsoon responded:  2019-11-29

Hi Brendan,
Thanks a lot for your help with the contacting Brian.
I created a post in the page of the project.

Thanks again.
Sunberg