IsoTracker: Change searching target #873
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Change the searching target from "same base seq and same mass" to "whatever but same seq"
We should choice the most ID, then use orderby.Last()
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #873 +/- ##
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+ Coverage 78.28% 78.32% +0.03%
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Files 244 245 +1
Lines 35726 35770 +44
Branches 3761 3763 +2
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+ Hits 27969 28017 +48
+ Misses 7123 7120 -3
+ Partials 634 633 -1
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A few comments:
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(1) add some tester for sorting function (2) revise the sorting function
…em-wisc/mzLib into IsoTracker_ChangeTarget
trishorts
requested changes
Apr 30, 2025
| public readonly Dictionary<SpectraFileInfo, List<ChromatographicPeak>> Peaks; | ||
| private readonly HashSet<string> _peptideModifiedSequencesToQuantify; | ||
| public IDictionary<string, Dictionary<PeakRegion, List<ChromatographicPeak>>> IsobaricPeptideDict = null; | ||
| public IDictionary<PeptideMassBin, Dictionary<PeakRegion, List<ChromatographicPeak>>> IsobaricPeptideDict = null; |
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I think this should be PeptideMzBin unless it is deconvoluted neutral mass. In that case, Mass is fine.
| internal List<PeptideMassBin> SortIsobaricPeptide(List<Identification> _allIdentifications, Tolerance massTolerance) | ||
| { | ||
| List<PeptideMassBin> isobaricPeptides = new List<PeptideMassBin>(); | ||
| var ids = _allIdentifications.Where(p => p.BaseSequence != p.ModifiedSequence).OrderBy(p => p.PeakfindingMass).ToList(); |
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can you add a comment explaining this restriction
| public double MaxMass { get; private set; } // The mass of the isobaric peptide | ||
| public List<Identification> Ids { get; set; } // The identification of the isobaric peptide | ||
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| public PeptideMassBin(Identification id, Tolerance tolerance) |
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i think you should specify the kind of tolerance (ppm or mass)
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The origin searching target is "the peptide with same base seq and same mass"
But the definition of an Isobaric peptide is "whatever peptide with the same mass"
So in this PR, we change the search target. The following are the changes I made:
(1) new class IsobaricPeptide that is used for store the isobaric peptide id and the mass range
(2) new tester to evaluate IsoTracker's ability to sort the peptide id into isobaricPeptide
(3) remove the redundant tester
(4) revised the peptideID merging function