Issue 259: Near isobars in spectral library building getting merged

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:2
Milestone:4.1
Opened:2013-08-09 by Brendan MacLean
Changed:2018-10-16 by Brendan MacLean
Resolved:2018-10-15 by Nick Shulman
Resolution:Fixed
Closed:2018-10-16 by Brendan MacLean
2013-08-09 Brendan MacLean
Title»Near isobars in spectral library building getting merged
Assigned To»Brendan MacLean
Notify»jjaffe;kaipot
Type»Defect
Area»Skyline
Priority»2
Milestone»2.1
Jake Jaffe highlighted a case where the following two reference lines and their attendant spectra get merged, and essentially only the first spectrum is represented.

full_spectral_library.ms2    6    2    T[56.0262]K[42.0470]QTAR[10.0083]
full_spectral_library.ms2    7    2    T[56.0262]K[42.0106]QTAR[10.0083]

The relevant modifications are propionyl (56.0262), trimethyl (42.0470), acetyl (42.0106), and SILAC R10 (10.0083) in this case.

Unfortunately, quite a lot inside Skyline currently assumes that amino acid and a single decimal place are sufficient to differentiate all known modifications (obviously not for this case).

Supporting the highlighted case will mean rethinking this assumption and fixing both library building and Skyline internal modification annotation to get this working.

2013-08-09 Brendan MacLean
Milestone2.1»3.1

2013-08-09 Brendan MacLean
Milestone3.1»

2017-08-31 Brendan MacLean
Assigned ToBrendan MacLean»kaipot@u.washington.edu
Notifyjjaffe;kaipot»jjaffe;kaipot;Nick Shulman
Milestone»4.1
I am going to assign this to Kaipo. I hope we can fix this with the new work on peptide modified sequence keys that Nick has taken over. Though, this may still require new work from Kaipo on the BlibBuild side.

2017-09-21 Kaipo
Assigned Tokaipot@u.washington.edu»Nick Shulman
Maybe something for Nick to think about as he has this hot potato now.

2018-10-15 Nick Shulman
resolve as Fixed
Statusopen»resolved
Assigned ToNick Shulman»Brendan MacLean
Notifyjjaffe;Kaipo;Nick Shulman»jjaffe;Nick Shulman
This got fixed in Skyline 4.1.

2018-10-16 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest