Brendan MacLean responded: |
2018-11-06 12:39 |
Sigh. It looks like we didn't quite get WIFF2 support (which was very last-minute) surfaced to Skyline. The work to expose it is relatively minimal, though, and I promise it will be a part of the first Skyline 4.2 patch release.
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sandberg responded: |
2018-11-14 00:58 |
Ok. Do you have any estimate of when this will happen?
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Brendan MacLean responded: |
2018-11-14 01:05 |
The fix will be in the next releases of both Skyline-daily and Skyline. It will be released first in Skyline-daily, probably by next Monday. I am teaching at the EMBL Targeted Proteomics course in Barcelona, so probably too busy to make a release before Saturday when I return to Seattle.
For an official Skyline release you likely will need to wait at least a couple more weeks, as we work to assemble multiple fixes we would like to release in the first patch to Skyline 4.2.
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sandberg responded: |
2018-11-14 01:40 |
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lund responded: |
2018-11-27 04:48 |
Hi!
Is there any news regarding wiff2 support?
Rikke
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Brendan MacLean responded: |
2018-11-27 06:37 |
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lund responded: |
2018-11-28 00:40 |
Hi Brendan
We have tested it but we were not able to get it to work.
We tried in two ways:
- Import DDA Peptide search, but were not able to import the wiff2 in the "Import Pepetide Search" step (skyline_wiff2_1). Wiff2 is not on the list and selecting a wiff2-file does not lead to any importing.
- Importing the file from file->import->results, this lead us a bit further (skyline_wiff2_2), but still no imported files.
I hope this helps you to figure out how to fix it :-)
Rikke
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Brendan MacLean responded: |
2018-11-28 07:37 |
Hi Rikke,
In the #1 case it looks like you somehow performed your Mascot search in a way that dropped the spectrum source file name, which is why you see it showing you the .dat name, and that name "18247_2_2000ppm.dat" does not match the basename of any of your .wiff2 files. The closest being "18247_2_2000ppm_20ug.wiff2". If you change the name of either the .dat or the .wiff2 to match, or you fix your search pipeline to store source file names in your Mascot searches (see https://skyline.ms/wiki/home/software/Skyline/page.view?name=mascot_missing_rt).
The type "ABSciex WIFF" should include both .wiff and .wiff2 now. Though, that should probably changed to "Sciex WIFF & WIFF2". Thanks for pointing that out. But also "Any spectra format" is clearly working in the image you sent, since I can see all your .wiff2 files. The problem is that none of them have a base name matching your .dat file, which is what Skyline is asking you to find.
As for the error in #2, we will look into that, if you can post an example file to:
https://skyline.ms/files.url
Thanks for testing our attempts to get WIFF2 support working for Skyline users.
--Brendan
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Brendan MacLean responded: |
2018-11-28 13:22 |
We do really need files to reproduce this. Ideally you would post both a Skyline document (File > Share - Complete to create a ZIP file) and a WIFF2 with data for your targets, but even having just the WIFF2 would help.
Again, just upload to:
http://skyline.ms/files.url
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lund responded: |
2018-11-29 04:57 |
Hi Brendan
Thanks a lot for looking into it so fast :-)
I have uploaded a zip file "for skyline" description: "files for wiff2 issue".
It should contain a complete wiff2 file, a skyline file, a mgf file generated by Proteowizard and a fasta-database.
Please let me know if you need more files or information
Rikke
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Matt Chambers responded: |
2018-11-29 07:41 |
OK. It only happens with the acceptZeroLengthSpectra mode that Skyline uses (but msconvert doesn't by default). It's a Sciex API bug, but we should be able to work around it. Thanks for the test file.
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lund responded: |
2018-12-03 00:22 |
Yeah! Have downloaded the new skyline daily. It also works with my original file!
Thanks :-)
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