Issue 72: Implement MS1 isotope values in reports

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:Skyline
Priority:3
Milestone:1.2
Opened:2011-07-23 by Brendan MacLean
Changed:2011-08-24 by Brendan MacLean
Resolved:2011-08-24 by Brendan MacLean
Resolution:Fixed
Closed:2011-08-24 by Brendan MacLean
2011-07-23 Brendan MacLean
Title»Implement MS1 isotope values in reports
Assigned To»Brendan MacLean
Notify»bschilling@buckinstitute.org mrardin@buckinstitute.org maccoss@u.washington.edu
Type»Todo
Area»Skyline
Priority»3
Milestone»1.2
Several MS1 isotope values have now been implemented in the Skyline UI, but not yet in the reports and results grid. This issue will serve to track their implementation. The values are:

PrecursorResult.IsotopeDotProduct or EnvelopeDotProduct
Transition.IsotopeEnvelopeProportion or EnvelopeProportion

From an earlier email about the naming of these fields and corresponding values in the UI, I wrote:

1. Expected - this is the name given an extra column in the Peak Area Replicate Comparison graph to show expected relative intensities of the isotope envelope transitions (for MS/MS spectral libraries am equivalent column is labeled "Library")
2. idotp - a new dot-product between the M, M+1, M+2, etc. transition peak areas and the expected distribution values in the predicted isotope envelope (dot-product between a MS/MS spectral library and product ion transitions appears as "dotp")
3. isotope_dotp - the name this value is given in the document XML (dot-product between a MS/MS spectral library and product ion transitions appears as "library_dotp")
4. ?? - should the raw expected proportion of the isotope envelope appear in the document XML (for MS/MS libraries, the XML contains <libinfo intensity=""/>), this would be purely informational, and recalculated at document open time, as are most transition values in the document XML, like m/z, CE, etc.
5. ?? - Need a name for the "idotp" value in reports and the results grid (for "dotp", LibraryDotProduct is used)
6. ?? - Need a name for the expected isotope envelope proportion for a transition (for MS/MS libraries, we currently have both Library Rank and Library Intensity - Q: should Skyline somehow try to show isotope peak rank, though it will most often be a straight 1, 2, 3 order, but not always)

The existing choices in 2 and 3 seem to imply "IsotopeDotProduct" in #5, but I am not sure about how clear this will make the new value, given the existing focus on the use of the term "isotope" for "Isotope modifications". It is strongly linked to stable isotope labeling. Using "isotope" for a different concept may confuse people. So, I am wondering if I shouldn't change to "envelope" producing the following names: #2 = edotp, #3 = envelope_dotp, #5 = EnvelopeDotProduct. #1 could either become "Envelope" or stay "Expected" and still have some connection with "edotp". Finally, #4 = envelope_proportion and #6 = EnvelopeProportion (0 - 1.0).



2011-07-26 Brendan MacLean
TitleImplement MS1 isotope values in reports»**Implement MS1 isotope values in reports
Fixed on my machine. This will be in the next release. After feedback from Mike I decided to go with "isotope distribution" terminology, shortened to IsotopeDist.

All current terms remain unchanged. The terms I have added are:

PrecursorResult.IsotopeDotProduct
Transition.IsotopeDistProportion

The latter hopefully gets across that it is the proportion of the entire isotope distribution, and not just of the included transitions.

I expect I will eventually also add Transition.IsotopeDistRank, which will be the equivalent of Transition.LibraryRank. That would have required more code, and didn't seem critical at this point.

2011-08-24 Brendan MacLean
resolve as Fixed
Title**Implement MS1 isotope values in reports»Implement MS1 isotope values in reports
Statusopen»resolved
Fixed and released.

2011-08-24 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest