While those tests are still running, I pulled out all 185 of the proteins
that are in the 10OV pepXMLs but not in 01-09OV, figuring that maybe one of
those is causing the error. I've uploaded that to the same folder
everything else is in (it's called 10OV_uniq.fasta) - I don't see anything
Hi Emily,
I analyzed the search results that you sent and I am seeing some strange
things in at least one of the files you gave me. This may be causing some
of the problems you saw.
In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line
171821 there are some strange characters
Hello,
Thanks so much for taking a look! I think the selenocysteines ("U") are
likely not the problem, since I've got those in all of my databases,
including the ones that run correctly. I'm looking at
03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see
anything odd in line
Hello,
Thanks so much for taking a look! I think the selenocysteines ("U") are
likely not the problem, since I've got those in all of my databases,
including the ones that run correctly. I'm looking at
03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see
anything odd in line
If you follow the link further
https://skyline.ms/wiki/home/software/Skyline/page.view?name=OverlappingWindowScheme&_docid=wiki%3A41195689-d578-1036-894e-e465a393d561
they explain how to actually make the isolation scheme in skyline that is
compatible with several MS manufacturers; I believe the
Hi all,
I have acquired a bunch of files on my Eclipse to build a DIA library using
an 8mz window in overlap mode (ie essentially 4mz windows) and I'm not
clear if the Convert to MzML is demultiplexing to 4mz windows? I've tried
doing it manually in MSconvert but the conversion fails. On the
Dear Jane,
I cannot help you with the demultiplexing, because I have not used that
feature before in MSConvert. But if you do manage to get a regular DIA
mzML file out of the conversion you can use the DISCo tool available in the
TPP under Tools->DIA->Extract MS2 Fragments that will generate a
Hey David!
Yes, I'd like to know more about DISCo. I was poking around that tool too
and kinda got lost :) That's what 3 years away from proteomics will do for
you! The MSconvert within TPP creates mzML files fine, I guess I don't
know how to check to see if they have been demultiplexed. Can
Jane,
See this from the Skyline team:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=DemultiplexingOverlappingDIAWindows
Best
Mark
On Thu, Oct 22, 2020 at 4:28 PM Science Gurl wrote:
> Hey David!
>
> Yes, I'd like to know more about DISCo. I was poking around that tool too
>
Hi Mark,
Thanks for the suggestion... This is what I've been doing but I get an
error. I'll switch this query to the SkyLine team for some more
troubleshooting!
-jane
On Thu, 22 Oct 2020 at 17:04, Mark Athanason
wrote:
> Jane,
>
> See this from the Skyline team:
>
>
I just re extracted that file and I don't see the issue anymore. Perhaps
this was a decompression issue.
Thanks for checking.
-David
On Thu, Oct 22, 2020 at 12:19 PM Emily Kawaler wrote:
> Hello,
> Thanks so much for taking a look! I think the selenocysteines ("U") are
> likely not the
Thanks!
On Thu, 22 Oct 2020 at 17:11, Mark Athanason
wrote:
> If you follow the link further
>
> https://skyline.ms/wiki/home/software/Skyline/page.view?name=OverlappingWindowScheme&_docid=wiki%3A41195689-d578-1036-894e-e465a393d561
>
> they explain how to actually make the isolation scheme in
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