wiki:glycanCentricView

Glycan Centric View

Requirements:

  1. Additional view for MS Glycan Annotation results (see image below)
  2. Create a nattable grid that uses column groups (by charge state) and row groups (by molecular weight)
  3. Collate information from 'scan-based' view and organize by molecular weight
  4. For each molecular weight, add rows for which a glycan feature was observed for each charge state
  5. For each charge state, include information like m/z, mass error, intensity, score, etc

Potential Problems and Proposed Solutions:

  1. If multiple MS2 scans match to the same structure and charge state, there is no obvious way to display the results in individual cells

Proposed solution: for m/z and error, use the average from all MS2. For scores, merge the MS2 spectra and score it as combined.

Proposed interaction and new result options

  1. The editor is broken down into 2 tables: top is the glycan-centric view, bottom is the peak selector table (as used in MS Glycan Annotation editor)
  2. Single-clicking on a Mass(m) cell fills the bottom table with all peak data that correspond to that Mass.
  3. Single-clicking on a Structure cell (cartoon) fills the bottom table with all peak data that correspond to that structure only.
  4. Single-clicking on a cell under a particular charge state fills the bottom table with all peak data that correspond to that structure + charge only.
  5. The selection table contains check boxes that allows the user to change the selected features for a particular scan. This will have to interact with the MS Glycan Annotation table. More to describe here.
  6. Double-clicking a row opens the MS Glycan Annotation Summary View so the user can view the matched fragments.
  7. Proposed new data type: "Unique score". When multiple structures match the same mass, many theoretical fragments are in common between the possible structures. If we remove the common fragments and score the fragments unique to each structure, this may help the user determine which structure is likely present.

Related images Mockup of proposed interface:

GlycanCentricView_mockupV1_1024.jpg

Photo of whiteboard from meeting with Rene, Mindy and Brent on 05/19/15.

Camera picture of whiteboard from meeting of Rene, Mindy, Brent

Last modified 7 years ago Last modified on 05/27/2015 10:03:32 PM

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