Issue 811: deal with the TODO from commit "When adding small molecule library values to a document, just ignore any fragment peaks with absurdly small or large m/z values"

issues
Status:open
Assigned To:Brian Pratt
Type:Defect
Area:Skyline
Priority:3
Milestone: 
Opened:2021-05-24 by Brian Pratt
Changed:2021-05-24 by Brian Pratt
Resolved:
Resolution:
Closed:
2021-05-24 Brian Pratt
Title»deal with the TODO from commit "When adding small molecule library values to a document, just ignore any fragment peaks with absurdly small or large m/z values"
Assigned To»Brian Pratt
Type»Defect
Area»Skyline
Priority»3
in pwiz_tools/Skyline/Model/AbstractModificationMatcher.cs

                    // Some kind of garbage in peaklist, e.g fragment mass is absurdly small or large - ignore
                    // TODO(bspratt) - address Brendan's comment from pull request:
                    // "This call should be paying attention to settings and the minimum value that causes the exception reported to initiate this fix.For peptide fragment
                    // annotation, we definitely consider the settings, and since we do not rank fragments outside the instrument range. This code also strikes me as odd that you wouldn't just create the precursor
                    // and then use a precursor.ChangeSettings(Settings, diff ?? SrmSettingsDiff.ALL) to materialize all of the transitions based on the settings. That way you only write the code once to materialize
                    // transitions based on settings."
                    // In particular not ranking things outside the machine range makes sense.