Issue 238: Add ability to import peptide search to SkylineRunner

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:Skyline
Priority:3
Milestone:3.2
Opened:2013-05-10 by Brendan MacLean
Changed:2016-01-06 by Brendan MacLean
Resolved:2016-01-06 by Brendan MacLean
Resolution:Fixed
Closed:2016-01-06 by Brendan MacLean
2013-05-10 Brendan MacLean
Title»Add ability to import peptide search to SkylineRunner
Assigned To»killeent@uw.edu
Type»Todo
Area»Skyline
Priority»3
Milestone»2.1
Recently posted to the support board by a Skyline user:

I'm thinking about the automatic pipeline that would build spectral library from replicate experiments and use it for MS1 quantitation of these experiments.

I can already automate the building of Spectral Libraries using BlibBuilder.exe. And also, once Skyline project is defined (i.e. Spectral Libraries and protein sequence database imported) I can import replicate MS experiments using SkylineRunner. The missing things are:
  1) the ability to specify spectral library for a Skyline project via SkylineRunner (when I look at .sky XML it looks like there is no way to specify the library by file location, it has to be registered from Skyline GUI; please correct me if I'm wrong)
  2) the ability to import FASTA sequence database via SkylineRunner

2013-05-10 Brendan MacLean
Notify»alyst

2013-05-13 Brendan MacLean
Assigned Tokilleent@uw.edu»kaipot@u.washington.edu
Decided Kaipo would be better for this, since he is already working in this code.

2013-06-06 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned Tokaipot@u.washington.edu»Brendan MacLean
Kaipo has implemented these additions and they have been released in 1.4.1.5600

2013-06-06 Brendan MacLean
reopen
Statusresolved»open
From Alexey:
One minor thing is that in the FASTA files import GUI the user is being asked if proteins that have no peptides in the spectral library should be discarded.
As far as I understand, there is no similar option in SkylineRunner, so all the proteins are kept, and that increases the size of .sky file by approximately 20Mb.
It would be nice to have an option/command to discard unreferenced proteins from the Skyline project to save the space and processing times.

Brendan: I think this should be the default, and we can add a flag that allows someone to keep everything, but I expect this to be an infrequently used option.

2014-01-08 Brendan MacLean
Milestone2.1»2.6
Didn't make v2.1. Next release.

2014-04-14 Brendan MacLean
Assigned ToBrendan MacLean»kaipot@u.washington.edu

2014-08-28 Brendan MacLean
Milestone2.6»3.1

2015-08-06 Brendan MacLean
Assigned Tokaipot@u.washington.edu»Brendan MacLean
Milestone3.1»3.2

2016-01-06 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Kaipo implemented this for Skyline 3.5.

2016-01-06 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest