Hi Skyline team,
I'm trying to import some data from my ABSciex 4000 QTRAP into Skyline. This is from a small molecule experiment using the QTRAP in Q1 Multiple ions (Q1 MI) mode. When I go to import my results, Skyline recognizes the .wiff files for my standards as results files, but when I try to actually import the files (File-->Import-->Results-->Add single injection reps...), I get the following error:
At 11:27 AM:
Failed importing results file 'C:\Users\jblakehedges\Documents\Proteomics\Small molecule test\Data Files\12.5uMpyrone-0.5uL-01.wiff'.
The sample 12.5uMpyrone-0.5uL-01 contains no usable data.
Inner exceptions:
Exception type: System.IO.InvalidDataException
Error message: The sample 12.5uMpyrone-0.5uL-01 contains no usable data.
The sample 12.5uMpyrone-0.5uL-01 contains no usable data.
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 277
I'm attaching the Skyline file that I'm trying to import into and also the data files I've tried and failed to import. This was performed both on my personal laptop (64-bit, Skyline v.4.1) and on the instrument computer (32-bit, Skyline v. 3.7), and both times I encountered the same error. Please help!
Thanks,
Jackie |
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| Nick Shulman responded: |
2018-04-06 11:59 |
I think your .wiff files really are empty.
The only thing that Skyline is able to see in your files is the Total Ion Chromatogram.
All of your .wiff files are 124KB, and your .wiff.scan files are 12KB.
.wiff files from SRM experiments are usually a little bigger than that, and .wiff.scan files are usually bigger than the corresponding .wiff files. |
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| jmblakehedges responded: |
2018-04-06 12:12 |
Yeah, they're a little small, but this is what the instrument is outputting for this type of experiment. Maybe they're small because we're only targeting 5 or so Q1 ions? I can open the files in Analyst (see attached screenshots), and the file size is the same as the size on the instrument computer. So, there's definitely something contained in here. Do you think there's any way you'll be able to make this compatible with Skyline? |
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| Matt Chambers responded: |
2018-04-06 13:07 |
The picture is of a SIM experiment, not SRM. Our WIFF file reader doesn't support that. That may just be because we'd never seen SIM data before. I can check the feasibility of reading it next week. |
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| Matt Chambers responded: |
2018-04-11 10:59 |
Hi Jackie,
I've added support for SIM data in a development branch. Is it alright if we use this tiny 50uMpyrone-8uL-01.wiff file for our automated tests? It's rare to find such tiny files and they are useful for testing!
Thanks,
-Matt |
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| jmblakehedges responded: |
2018-04-11 15:59 |
Hi Matt,
Yes, please feel free to use those files as tests, and let me know if you'd like some more to play around with. We have plenty of tiny files from small molecule experiments that we could send your way. Looking forward to hearing if it works!
Thanks,
Jackie |
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20180406_lactones stds test_d.sky.zip
50uM pyrone_in Analyst.png
50uM pyrone_file size_QTRAP computer.png