Issue 212: Add filter exclusion for peptide duplication

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:Skyline
Priority:3
Milestone:3.1
Opened:2012-12-13 by Brendan MacLean
Changed:2017-06-08 by Brendan MacLean
Resolved:2017-06-08 by Brendan MacLean
Resolution:Fixed
Closed:2017-06-08 by Brendan MacLean
2012-12-13 Brendan MacLean
Title»Add filter exclusion for peptide duplication
Assigned To»Brendan MacLean
Type»Todo
Area»Skyline
Priority»3
Milestone»2.1
The ability to filter peptides in the settings by whether or not they are "unique" to a background proteome has been requested. Unfortunately, this feature probably requires a better definition of uniqueness than is possible with the current background proteome implementation. We would need to introduce the concept of source genes for each protein in order to avoid letting multiple isoforms for the same gene cause peptide exclusion, and even an inability to find uniquely identifying peptides for a FASTA sequence with a very similar isoform.

Once we can produce source gene information for each FASTA sequence, this would be a very useful feature to add to Skyline.

2014-01-08 Brendan MacLean
Assigned ToBrendan MacLean»bspratt
Milestone2.1»2.6
It seems like you are working on the gene information part of this. This past summer an important group requested that we just add a checkbox to the settings (probably under the background proteome) that tells us to filter for uniqueness based solely on the FASTA ID, since some FASTA files (like UniProt) should support this. By waiting until we can solve all cases, we are apparently making life more difficult for a relatively common and simple case to solve.

So, probably solve this issue in two phases:
1. Add the checkbox
2. Do something more complete when we have gene information

2014-02-04 Brendan MacLean
Priority3»2

2014-02-04 Brendan MacLean
Priority2»3

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

2017-06-08 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned ToBrian Pratt»Brendan MacLean
I think this was fixed a long time ago.

2017-06-08 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest