[FIX] use MS2 spec for quant purity, return purity=1 for empty window…

…, fix ppm bug
jpfeuffer · Mar 18, 2024 · 09f02c4 · 09f02c4
1 parent 7d9c40f
commit 09f02c4
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Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/src/openms/source/ANALYSIS/ID/PrecursorPurity.cpp b/src/openms/source/ANALYSIS/ID/PrecursorPurity.cpp
@@ -6,6 +6,7 @@
 // $Authors: Eugen Netz $
 // --------------------------------------------------------------------------
 
+#include "OpenMS/METADATA/InstrumentSettings.h"
 #include <OpenMS/ANALYSIS/ID/PrecursorPurity.h>
 #include <OpenMS/CONCEPT/Constants.h>
 #include <OpenMS/CONCEPT/LogStream.h>
@@ -23,8 +24,8 @@ namespace OpenMS
   {
     const auto& ms2_spec = exp[ms2_spec_idx];
     const auto& precursor_spec = exp[precursor_spec_idx];
-    std::vector<double> purities(ms2_spec.getPrecursors().size(), 0.0);
-    if (precursor_spec.empty()) return purities;
+    std::vector<double> purities(ms2_spec.getPrecursors().size(), 1.0);
+    if (precursor_spec.empty()) return purities; // TODO fail instead?
 
     Size precursor_idx = 0;
     for (const auto& precursor_info : ms2_spec.getPrecursors())
@@ -37,9 +38,14 @@ namespace OpenMS
       // the actual boundary values
       const double strict_lower_mz = precursor_info.getMZ() - precursor_info.getIsolationWindowLowerOffset();
       const double strict_upper_mz = precursor_info.getMZ() + precursor_info.getIsolationWindowUpperOffset();
+      if (strict_lower_mz == strict_upper_mz)
+      {
+        return purities;
+      }
 
-      const double fuzzy_lower_mz = strict_lower_mz - Math::getPPM(strict_lower_mz, max_precursor_isotope_deviation);
-      const double fuzzy_upper_mz = strict_upper_mz + Math::getPPM(strict_upper_mz, max_precursor_isotope_deviation);
+      const double dev_ppm = max_precursor_isotope_deviation / 1e6;
+      const double fuzzy_lower_mz = strict_lower_mz * (1 - dev_ppm);
+      const double fuzzy_upper_mz = strict_upper_mz * (1 + dev_ppm);
 
       // first find the actual precursor peak
       Size precursor_peak_idx = precursor_spec.findNearest(precursor_info.getMZ());
@@ -197,7 +203,6 @@ namespace OpenMS
     const auto& ms2_spec = exp[ms2_spec_idx];
     const auto& precursor_spec = exp[precursor_spec_idx];
     const auto& next_ms1_spec = exp[next_ms1_spec_idx];
-    const auto& precursor_info = ms2_spec.getPrecursors()[0];
     // compute purity of preceding ms1 scan
     std::vector<double> early_scan_purity = computeSingleScanPrecursorPurities(ms2_spec_idx, precursor_spec_idx, exp, max_precursor_isotope_deviation);
     std::vector<double> late_scan_purity  = computeSingleScanPrecursorPurities(ms2_spec_idx, next_ms1_spec_idx, exp, max_precursor_isotope_deviation);

diff --git a/src/openms/source/MATH/MISC/NonNegativeLeastSquaresSolver.cpp b/src/openms/source/MATH/MISC/NonNegativeLeastSquaresSolver.cpp
@@ -18,7 +18,7 @@ namespace OpenMS
     int a_rows = (int)A.rows();
     int a_cols = (int)A.cols();
 
-    if (a_rows != b.size())
+    if (a_rows != (int) b.size())
     {
       throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "NNSL::solve() #rows of A does not match #rows of b !");
     }

diff --git a/src/topp/IsobaricWorkflow.cpp b/src/topp/IsobaricWorkflow.cpp
@@ -256,7 +256,7 @@ class TOPPIsobaricWorkflow :
     if (has_ms3)
     {
       // TODO double-check that this is the correct way to compute the purity for MS3. Currently purities are very low.
-      std::vector<double> quant_purities = PrecursorPurity::computeSingleScanPrecursorPurities(quant_spec_idx, ms1_spec_idx, exp, max_precursor_isotope_deviation);
+      std::vector<double> quant_purities = PrecursorPurity::computeSingleScanPrecursorPurities(quant_spec_idx, id_spec_idx, exp, max_precursor_isotope_deviation);
       // average over all precursors
       quant_purity = std::accumulate(quant_purities.begin(), quant_purities.end(), 0.0) / quant_purities.size();
     }