Issue 576: Creating Reports: atomic composition (formula) does not contain stable isotope info

issues
Status:resolved
Assigned To:Brian Pratt
Type:Defect
Area:Skyline
Priority:3
Milestone:4.1
Opened:2018-05-28 by henrik molina
Changed:2018-06-01 by Brian Pratt
Resolved:2018-06-01 by Brian Pratt
Resolution:Fixed
Closed:
2018-05-28 henrik molina
Title»Creating Reports: atomic composition (formula) does not contain stable isotope info
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
Milestone»4.1
Dear Skyline Team,

When creating a report (small molecule analysis) I can not pass out the stable isotope based formula associated with a molecule.
Though mass is correct for a labelled molecule the chemical formula is w/o the stable isotope info. Am I missing something?

Best, h

2018-05-28 Brendan MacLean
Assigned ToBrendan MacLean»Brian Pratt
I find myself a little stumped as well. When I run the small molecule tutorial test and stop to view the Precursors report in the Document Grid, this is what I see:

Precursor    Peptide    Precursor Ion Formula    Precursor Neutral Formula
150.0583[M+H]    Methionine    C5H11NO2S    C5H11NO2S
153.0772[M3H2+H] (heavy)    Methionine    C5H11NO2S    C5H11NO2S

I can't see how the Precursor Ion Formula and the Neutral Formula for both heavy and light can all be the same. Let's say the neutral light formula is C5H11NO2S, then I would expect the ion formula to be C5H12NO2S, since the adduct indicates the ion has +H, and I would expect the neutral heavy formula to be C5H'3H8NO2S (since the adduct indicates 3H2 or 3 deuterium atoms) and the ion heavy formula to be C5H'3H9NO2S.

Am I mistaken in what I am expecting to see?

2018-05-29 Brian Pratt
Certainly not behaving as one would reasonable expect - probably a hangover from the time before we had a proper "neutral molecule + adduct" model and there was no real distinction between the molecule and its precursor ion.

I agree that the "Ion Formula" would be reasonably expected to be the neutral formula with the adduct applied, including any isotopic labels. So, the case of

153.0772[M3H2+H] (heavy) Methionine C5H11NO2S C5H11NO2S

it should really be

153.0772[M3H2+H] (heavy) Methionine C5H'3H9NO2S C5H11NO2S

2018-05-29 Brian Pratt
Note that the neutral formula does *not* include the labels. Those are part of the adduct description,:think of them as "modifications" in the peptide sense. We track the neutral molecule as the link between labeled and unlabeled versions for quantification.

2018-05-29 Brian Pratt
Here's some actual Skyline output with my proposed fix:

Molecule Name,Molecule Formula,Precursor Ion Formula,Precursor Neutral Formula,Precursor Adduct,Precursor Mz,Precursor Charge
12-HETE,C20H32O3,C20H31O3,C20H32O3,[M-H],319.227869,-1
12-HETE,C20H32O3,C20H23H'8O3,C20H32O3,[M8H2-H],327.278083,-1

2018-05-29 Brian Pratt
Or rather, this. The isotopic labels appear in Precursor Neutral Formula, the labels and ionization appear in the Precursor Ion Formula, and neither appear in the Molecule Formula.

Molecule Name,Molecule Formula,Precursor Ion Formula,Precursor Neutral Formula,Precursor Adduct,Precursor Mz,Precursor Charge
12-HETE,C20H32O3,C20H31O3,C20H32O3,[M-H],319.227869,--1
12-HETE,C20H32O3,C20H23H'8O3,C20H24H'8O3,[M8H2-H],327.278083,-1

2018-06-01 Brian Pratt
resolve as Fixed
Statusopen»resolved