Build spectral library from Byonic searching results

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Build spectral library from Byonic searching results Qiongyu  2017-12-15 12:29
 
Hi,
I used the mizd files exported from Byonic to build a spectral library. My file name is:

***.raw_20171214_Byonic.mzid

However, after I added those files, an error came out.
The error says:

Cound not find spectrum file
***.raw_20171214_Byonic[MGF|.mzXML|.mzML] in current directory.

My Skyline is version 3.7.0.10940.

I am kind of confused now. I thought that among mzid, mgf, mzXML, and mzML files, mzid file is the only type of file that can be used to build a spectral library. But why is the file shown in the error has those other extensions?
How can I fix this problem?
Best,
Qiongyu
 
 
Brian Pratt responded:  2017-12-15 12:45
The spectral library builder needs both the search result file and the file that was searched to make the spectral library. It tries to locate the searched by replacing the search result file extension (.mzid in this case) with known mass spec file extensions (.MGF or .mzXML or .mzML) but in this case found no match for any of those.

I hope this makes sense?

Brian Pratt
 
Qiongyu responded:  2017-12-15 13:27
So that I need to put those searched files in the same folder, I guess?
Thank you!
 
Brian Pratt responded:  2017-12-15 13:40
That's correct.

Thanks for using the Skyline support board!

Brian
 
Qiongyu responded:  2017-12-15 14:04
I converted my RAW data collected from Orbitrap into mzXML files and put them in the same fold where my mzid files are. However, after a while, it came an error again saying that: No spectra were found for the new library.
Did I miss anything?
Thank you!
Best,
Qiongyu
 
Brendan MacLean responded:  2017-12-15 14:11
Open the mzid file in a text editor and make sure the names in the mzid file match the names of your mzXML. The error is a bit strange:

Cound not find spectrum file
***.raw_20171214_Byonic[MGF|.mzXML|.mzML] in current directory.

This would seem to indicate that Skyline is looking for:

.raw_20171214_ByonicMGF
.raw_20171214_Byonic.mzXML
.raw_20171214_Byonic.mzML

I doubt you have a file by any of these names. I am unsure whether this is a bug in the error message or something in the mzid file that is unexpected and getting parsed incorrectly.

--Brendan
 
Kaipo Tamura responded:  2017-12-15 14:27
Hi Qiongyu,
Do you mind sharing the mzid and mzXML files with me so I can take a look at them? If you need a place to upload them, you can put them here: https://skyline.ms/files.url

Thanks,
Kaipo
 
Qiongyu responded:  2017-12-15 14:41
Hi Kaipo,
I dropped the zip file to the link you send to me. See if you can find them.
Best,
Qiongyu
 
Kaipo Tamura responded:  2017-12-15 15:18
Hi Qiongyu,
I don't see any files in there from you - could you try uploading it again?

Thanks,
Kaipo
 
Qiongyu responded:  2017-12-15 15:41
Hi Kaipo,
When I was trying to drop my files to the drop box, the website did not have any reactions... I don't know how should I upload my files.
Thank you for your help.
Best,
Qiongyu
 
Nick Shulman responded:  2017-12-15 16:32
Hi, Qiongyu,

On the page https://skyline.ms/files.url there is a button that says "Upload Files". When you push that button, it makes a file upload control appear, which has a "Browse" button which you can use to find the file that you want to upload.
(see attached image "HowToUploadFile.png")
 
Qiongyu responded:  2017-12-18 11:55
Hi Nick,
The file uploading page that I entered through your link doesn't have button says "Upload Files". It actually a blank page on which I can do nothing. Why is that the case?
Thank you!
Best,
Qiongyu
 
Nick Shulman responded:  2017-12-18 12:24
It looks like that page does not work in the Microsoft Edge browser.
I will try to figure out what is going wrong.

In the meantime, can you use a different browser such as Chrome or Firefox? It should work there.
 
Qiongyu responded:  2017-12-18 16:19
Hi Nick,
I finally uploaded my files using Chrome. It has my name in the file name and the description of the file is the same as the subject of this post.
Thank you!
Best,
Qiongyu
 
Qiongyu responded:  2018-01-02 13:20
Hi,
I am wondering if you have time to check the files that I uploaded to the folder?
Thank you!
 
Kaipo Tamura responded:  2018-01-02 15:44
Hi Qiongyu,
Sorry for the delay - I have reproduced your error and will work on a fix.

Thanks,
Kaipo
 
Qiongyu responded:  2018-01-03 15:14
Thank you!
 
Kaipo Tamura responded:  2018-01-05 15:19
I've committed a fix for this issue and it will be available in the next release of Skyline-daily.

Thanks,
Kaipo
 
Qiongyu responded:  2018-01-05 15:26
Thank you a lot Kaipo! I will try it soon.
 
Qiongyu responded:  2018-01-09 10:54
Hi Kaipo,
I tried to use mzid files to build the library and the software version is 3.7.0.11317. Is that the version for which you fix the problem?
Thank you!
Best,
Qiongyu
 
Kaipo Tamura responded:  2018-01-09 11:30
Hi Qiongyu,
The fix is in the current daily version of Skyline (4.0.9.11707). Skyline-daily is distinct from the main release, you can download it by going to the Skyline page (https://skyline.ms/project/home/software/Skyline/begin.view) and clicking the "Skyline-daily (beta)" button.

Thanks,
Kaipo
 
Qiongyu responded:  2018-01-09 17:47
It's working now. Thank you very much!