Issue 103: Implement support for MS3 full-scan filtering for neutral losses

Assigned To:Guest
Opened:2011-11-02 by Brendan MacLean
Changed:2018-10-16 by Brendan MacLean
Resolved:2018-10-16 by Brendan MacLean
Resolution:Won't Fix
Closed:2018-10-16 by Brendan MacLean
2011-11-02 Brendan MacLean
Title»Implement support for MS3 full-scan filtering for neutral losses
Assigned To»Brendan MacLean
On ion traps it is frequently necessary to collect MS3 spectra when targeting peptides with prominent neutral loss ions. This phenomenon happens more frequently on ion traps, because once the loss occurs the resulting fragment is off resonance and no further fragmentation occurs. To get more complete fragmentation, the loss ion must be isolated and then fragmented through MS3.

Skyline full-scan filtering should support this case with the following added features:
- A droplist should be added to the MS/MS filtering section:

  Filter neutral loss precursors in MS3:
  [ None [\/]

  Manual would allow loss precursors to be added to the document manually through a UI described below.
  Automatic would generate all possible loss precursor similar to variable modifications.

- If either Manual or Automatic is chosen in the Full-Scan settings, then a new menu item like Edit / Modify Peptide would be added (something like Edit / Modify Peptide Losses or Modify Losses on the right-click menu). It would only be available for peptides with modifications supporting neutral losses. The form UI would also be similar to the Modify Peptide form, with vertical display of the peptide sequence, and droplists beside the amino acids with neutral loss modifications. The user could choose which losses in MS/MS they are testing for. This would in turn affect the available fragment ion losses for the precursor.

Once this UI and the model to support it are implemented, it should be possible to interrogate the model during both method export and chromatogram filtering during import to both generate MS3 scans in the exported methods and filter product ions from MS3 scans respectively.

2014-01-08 Brendan MacLean

2018-10-16 Brendan MacLean
resolve as Won't Fix
This has been around for a long time without much movement. We are going to need a more compelling use case or data set requiring this.

2018-10-16 Brendan MacLean
Assigned ToBrendan MacLean»Guest