Issue 36: Import spectral libraries in .csv format (e.g. created from SRM atlas)

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:BiblioSpec
Priority:3
Milestone:2.6
Opened:2011-07-07 by Brendan MacLean
Changed:2014-08-28 by Brendan MacLean
Resolved:2014-08-28 by Brendan MacLean
Resolution:Fixed
Closed:2014-08-28 by Brendan MacLean
2011-07-07 Brendan MacLean
Title»Import spectral libraries in .csv format (e.g. created from SRM atlas)
Assigned To»frewen@u.washington.edu
Type»Defect
Area»Skyline
Priority»3
Milestone»1.2
It would be great if it was possible to construct an import feature for csv files in which users can specify peak masses, identities and relative peak intensities. For me it would be practical if such files could be imported into skyline and used as a sort of a spectral library. E.g. to verify the relative intensities of the transitions I measured.
  
The format we are using is the tsv of the SRMatlas transitions in a slightly modified form (see last slide in powerpoint). We can then import this file as a spectral library into Pinpoint 2.0. I thought it would be useful to have a csv import feature in Skyline. If it is exactly in the format we are using or in a more general one does not matter.

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The PowerPoint slides were lost in the hard-drive crash.

2011-07-07 Brendan MacLean
AreaSkyline»BiblioSpec

2013-04-02 Brendan MacLean
Assigned Tofrewen@u.washington.edu»kaipot@u.washington.edu
This is a pretty old one. I am not sure if it is applicable anymore. BlibBuild does support a .ssl format.

This support request provides some interesting information on the SSL format:

https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?entityId=234f81c4-5827-1030-b663-5d0a05bcf5f8&_docid=thread%3A234f81c4-5827-1030-b663-5d0a05bcf5f8

Could you help me make the call on whether SSL covers this request? Also, could you update the SSL documentation to fix the problem that caused this support request.

Thanks.

2013-08-17 Brendan MacLean
TypeDefect»Todo
Milestone1.2»2.2
I think I ended up doing something similar to this for the mProphet gold standard data set. I just wrote a converter from the format to SSL and MS2. If SRMAtlas is similar, it might be interesting to support.

2014-01-08 Brendan MacLean
Milestone2.2»2.6

2014-08-28 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned Tokaipot@u.washington.edu»Brendan MacLean
I think this should have been handled by Dario's new assay library import support.

2014-08-28 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest