Waters Data Importing Fail After 4.1.1.11871 Update

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Waters Data Importing Fail After 4.1.1.11871 Update StevenVds  2018-03-26 00:52
 
Hey Skyline,

I just did the 4.1.1.11871 skyline daily update released on the 24th op March. I work with Windows 10 Enterprise v. 10.0.15063 Build 15063.

I imported waters data like I usually do but this time I get following error message:
"At 09:43:
Failed importing results file 'S:\SKYLINE\Synapt\Skyline_Data\2018\QCspH7_191_220318_01n.raw'.
[pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Code"

I see that there is a new Waters data reader, maybe this can be the cause of the error?

Cheers
Steven Vds
 
 
Matt Chambers responded:  2018-03-26 08:11
Hi Steven,

If that file doesn't contain any secret data, can you upload this file to https://skyline.ms/filecontent/home/support/file%20sharing/begin.view?

It certainly seems likely that the Waters DLL upgrade is causing this, but I'll need to try to reproduce and if I can't figure out the cause, report it up the chain to Waters.

Thanks,
-Matt
 
StevenVds responded:  2018-03-27 06:26
I uploaded one of the files where I get the error. I mistakenly uploaded a 7z file first, sorry for that. The second file I uploaded is a zip file.

Cheers
Steven Vds
 
Brian Pratt responded:  2018-03-27 07:44
Hi Steven,

I'm not able to find a problem with that file on its own (that is , with msconvert or SeeMS) - can you also provide the Skyline document? Just use the File > Share > Complete menu item in Skyline, and upload the resulting .sky.zip file to the same location as the raw file.

Thanks,

Brian Pratt
 
StevenVds responded:  2018-03-27 08:07
Hi hi

The file should be available for you guys.

SVds
 
Brian Pratt responded:  2018-03-27 08:33
Got it, thanks, and I am able to reproduce the problem. We'll get this sorted out ASAP.

Am I correct in understanding that the problem was found just that one file of the many already imported to the document?

Thanks,

Brian
 
StevenVds responded:  2018-03-27 23:54
Hey Brian

All the files that are already in the document where imported before the update and went without any problem. It is indeed that one file the give a problem after the update (and also other Waters.raw files that I tried to import after the update).

Cheers
Steven Vds
 
Brian Pratt responded:  2018-03-28 08:51
Hi Steven,

We have reported the problem to Waters, as it does seem to stem from changes in the most recent reader DLL they've supplied. Specifically, FWIW, the problem appears to be in the area of centroiding.

Can you provide any detail about how the files were acquired that might help us help them to sort this out?

Thanks,

Brian
 
StevenVds responded:  2018-03-29 04:35
Hey Brian

The data is acquired in centroided mode... but if I'm correct then you should be able to find all the information in the raw file of that one run uploaded.

Steven Vds
 
Brian Pratt responded:  2018-03-29 08:10
That's very useful information, thanks. Presumably the Waters DLL is objecting to being asked to centroid already-centroided data - that's a new behavior but one I expect we can work with. Hopefully the new API helps with detecting this condition, we'll look into it.
 
Matt Chambers responded:  2018-03-29 08:46
Yes, Brian's intuition is right. The latest update was the first one with Waters centroid capability. In this current version, if Skyline is configured to do centroiding on already-centroided data, this error is the result. The next version will have this fixed. In the meantime you can either turn off centroiding in Skyline, or convert your files to mzML first.