From 853a5f7d5235198e7b84cfc518e01c5d45515a79 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Wed, 8 Feb 2023 11:41:54 -0500 Subject: [PATCH 01/14] - added automatic doubling of SIM/SRM RTWindows if a WIFF file was collected by SCIEX OS version less than 3.1 (reported by Phillip) * removed very old conditional code for .NET < 4 --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 52 +++++++++++-------- 1 file changed, 29 insertions(+), 23 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 118873572f..6b7b437ff0 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -36,6 +36,7 @@ #include #include #include +#include #pragma managed #include "pwiz/utility/misc/cpp_cli_utilities.hpp" @@ -48,10 +49,8 @@ using namespace Clearcore2::Data::AnalystDataProvider; using namespace Clearcore2::Data::Client; using namespace Clearcore2::Data::DataAccess; using namespace Clearcore2::Data::DataAccess::SampleData; - -#if __CLR_VER > 40000000 // .NET 4 using namespace Clearcore2::RawXYProcessing; -#endif +namespace bxp = boost::xpressive; // peak areas from Sciex are very small values relative to peak heights; // multiplying them by this scaling factor makes them more comparable @@ -147,6 +146,7 @@ struct ExperimentImpl : public Experiment const WiffFileImpl* wifffile_; gcroot msExperiment; int sample, period, experiment; + bool hasHalfSizeRTWindow; ExperimentType experimentType; size_t simCount; @@ -203,10 +203,7 @@ struct SpectrumImpl : public Spectrum ExperimentImplPtr experiment; gcroot spectrumInfo; mutable gcroot spectrum; - -#if __CLR_VER > 40000000 // .NET 4 mutable gcroot^> peakList; -#endif int cycle; @@ -241,11 +238,7 @@ WiffFileImpl::WiffFileImpl(const string& wiffpath) { try { -/*#if __CLR_VER > 40000000 // .NET 4 - Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; -#else - Licenser::LicenseKey = ABI_BETA_LICENSE_KEY; -#endif*/ + //Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; provider = DataProviderFactory::CreateDataProvider("", true); //provider = gcnew AnalystWiffDataProvider(); @@ -439,6 +432,25 @@ ExperimentImpl::ExperimentImpl(const WiffFileImpl* wifffile, int sample, int per transitionCount = msExperiment->Details->MassRangeInfo->Length; else if (experimentType == SIM) simCount = msExperiment->Details->MassRangeInfo->Length; + + hasHalfSizeRTWindow = false; + try + { + auto softwareVersion = ToStdString(wifffile_->batch->GetSample(sample)->Details->SoftwareVersion); + bxp::sregex sciexOsVersionRegex = bxp::sregex::compile(R"(SCIEX OS (\d+)\.(\d+))"); + + bxp::smatch match; + if (bxp::regex_match(softwareVersion, match, sciexOsVersionRegex)) + { + int major = lexical_cast(match[1].str()); + int minor = lexical_cast(match[2].str()); + hasHalfSizeRTWindow = !(major >= 3 && minor >= 1); // currently assumed present in SCIEX OS lower than v3.1 + } + } + catch (Exception^) + { + // ignore read past end of stream: no version details? probably acquired with Analyst? + } } CATCH_AND_FORWARD } @@ -523,11 +535,12 @@ void ExperimentImpl::getSIM(size_t index, Target& target) const SIMMassRange^ transition = (SIMMassRange^) msExperiment->Details->MassRangeInfo[index]; + double rtWindowMultiplier = hasHalfSizeRTWindow ? 1 : 0.5; target.type = TargetType_SIM; target.Q1 = transition->Mass; target.dwellTime = transition->DwellTime; - target.startTime = transition->ExpectedRT - transition->RTWindow / 2; - target.endTime = transition->ExpectedRT + transition->RTWindow / 2; + target.startTime = transition->ExpectedRT - transition->RTWindow * rtWindowMultiplier; + target.endTime = transition->ExpectedRT + transition->RTWindow * rtWindowMultiplier; target.compoundID = ToStdString(transition->Name); auto parameters = transition->CompoundDepParameters; @@ -561,12 +574,13 @@ void ExperimentImpl::getSRM(size_t index, Target& target) const MRMMassRange^ transition = (MRMMassRange^) msExperiment->Details->MassRangeInfo[index]; + double rtWindowMultiplier = hasHalfSizeRTWindow ? 1 : 0.5; target.type = TargetType_SRM; target.Q1 = transition->Q1Mass; target.Q3 = transition->Q3Mass; target.dwellTime = transition->DwellTime; - target.startTime = transition->ExpectedRT - transition->RTWindow; - target.endTime = transition->ExpectedRT + transition->RTWindow; + target.startTime = transition->ExpectedRT - transition->RTWindow * rtWindowMultiplier; + target.endTime = transition->ExpectedRT + transition->RTWindow * rtWindowMultiplier; target.compoundID = ToStdString(transition->Name); auto parameters = transition->CompoundDepParameters; @@ -768,23 +782,19 @@ size_t SpectrumImpl::getDataSize(bool doCentroid, bool ignoreZeroIntensityPoints if (experimentType == MRM || experimentType == SIM) return experiment->msExperiment->Details->MassRangeInfo->Length; -#if __CLR_VER > 40000000 // .NET 4 if (doCentroid) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); return (size_t) peakList->Length; } else -#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); -#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); -#endif } return (size_t) spectrum->NumDataPoints; } @@ -797,7 +807,6 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, { try { -#if __CLR_VER > 40000000 // .NET 4 if (doCentroid && pointsAreContinuous) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); @@ -812,15 +821,12 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, } } else -#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); -#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); -#endif } // XValues are not m/z values for MRM and SIM experiments From e3135e35620e13b09dac9c02db13c925b75d98e3 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Wed, 8 Feb 2023 16:14:46 -0500 Subject: [PATCH 02/14] * restored .NET < 4 checks to see if that has something to do with installer test failures --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 21 +++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 6b7b437ff0..baf798772d 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -49,8 +49,10 @@ using namespace Clearcore2::Data::AnalystDataProvider; using namespace Clearcore2::Data::Client; using namespace Clearcore2::Data::DataAccess; using namespace Clearcore2::Data::DataAccess::SampleData; + +#if __CLR_VER > 40000000 // .NET 4 using namespace Clearcore2::RawXYProcessing; -namespace bxp = boost::xpressive; +#endif // peak areas from Sciex are very small values relative to peak heights; // multiplying them by this scaling factor makes them more comparable @@ -203,7 +205,10 @@ struct SpectrumImpl : public Spectrum ExperimentImplPtr experiment; gcroot spectrumInfo; mutable gcroot spectrum; + +#if __CLR_VER > 40000000 // .NET 4 mutable gcroot^> peakList; +#endif int cycle; @@ -238,7 +243,11 @@ WiffFileImpl::WiffFileImpl(const string& wiffpath) { try { - //Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; +/*#if __CLR_VER > 40000000 // .NET 4 + Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; +#else + Licenser::LicenseKey = ABI_BETA_LICENSE_KEY; +#endif*/ provider = DataProviderFactory::CreateDataProvider("", true); //provider = gcnew AnalystWiffDataProvider(); @@ -782,19 +791,23 @@ size_t SpectrumImpl::getDataSize(bool doCentroid, bool ignoreZeroIntensityPoints if (experimentType == MRM || experimentType == SIM) return experiment->msExperiment->Details->MassRangeInfo->Length; +#if __CLR_VER > 40000000 // .NET 4 if (doCentroid) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); return (size_t) peakList->Length; } else +#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); +#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); +#endif } return (size_t) spectrum->NumDataPoints; } @@ -807,6 +820,7 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, { try { +#if __CLR_VER > 40000000 // .NET 4 if (doCentroid && pointsAreContinuous) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); @@ -821,12 +835,15 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, } } else +#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); +#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); +#endif } // XValues are not m/z values for MRM and SIM experiments From ab353adffd4eb0d98f4891e82ca4ca16101ecffe Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Thu, 9 Feb 2023 16:16:08 -0500 Subject: [PATCH 03/14] * switched from xpressive to .NET Regex --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index baf798772d..23eb606892 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -36,14 +36,15 @@ #include #include #include -#include #pragma managed #include "pwiz/utility/misc/cpp_cli_utilities.hpp" #include +#using #using using namespace pwiz::util; using namespace System; +using namespace System::Text::RegularExpressions; using namespace Clearcore2::Data; using namespace Clearcore2::Data::AnalystDataProvider; using namespace Clearcore2::Data::Client; @@ -445,15 +446,17 @@ ExperimentImpl::ExperimentImpl(const WiffFileImpl* wifffile, int sample, int per hasHalfSizeRTWindow = false; try { - auto softwareVersion = ToStdString(wifffile_->batch->GetSample(sample)->Details->SoftwareVersion); - bxp::sregex sciexOsVersionRegex = bxp::sregex::compile(R"(SCIEX OS (\d+)\.(\d+))"); + auto softwareVersion = wifffile_->batch->GetSample(sample)->Details->SoftwareVersion; + auto sciexOsVersionRegex = gcnew Regex(R"(SCIEX OS (\d+)\.(\d+))"); - bxp::smatch match; - if (bxp::regex_match(softwareVersion, match, sciexOsVersionRegex)) + auto match = sciexOsVersionRegex->Match(softwareVersion); + if (match->Success) { - int major = lexical_cast(match[1].str()); - int minor = lexical_cast(match[2].str()); + int major = Convert::ToInt32(match->Groups[1]->Value); + int minor = Convert::ToInt32(match->Groups[2]->Value); hasHalfSizeRTWindow = !(major >= 3 && minor >= 1); // currently assumed present in SCIEX OS lower than v3.1 + //if (hasHalfSizeRTWindow) + // Console::Error->WriteLine("NOTE: data from " + softwareVersion + " has bugged half-width RTWindows"); } } catch (Exception^) From 1518511e87c52c3e3ce672e3fae0926d55d1d34b Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Fri, 10 Feb 2023 11:25:02 -0500 Subject: [PATCH 04/14] - added start/end cycle override for SIM/SRM XICs from WIFF --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 28 ++++++++++--------- .../msrc/utility/vendor_api/ABI/WiffFile.hpp | 2 +- .../msrc/utility/vendor_api/ABI/WiffFile2.ipp | 5 ++-- 3 files changed, 19 insertions(+), 16 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 23eb606892..0229ff78ab 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -130,7 +130,7 @@ struct ExperimentImpl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const; @@ -609,14 +609,24 @@ void ExperimentImpl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const { try { if (index >= transitionCount+simCount) - throw std::out_of_range("[Experiment::getSIC()] index out of range"); + throw std::out_of_range("[Experiment::getSIC()] index " + lexical_cast(index) + " out of range"); + + Target target; + getSRM(index, target); ExtractedIonChromatogramSettings^ option = gcnew ExtractedIonChromatogramSettings(index); + if (target.startTime != target.endTime) + { + option->StartCycle = convertRetentionTimeToCycle(target.startTime); + option->EndCycle = convertRetentionTimeToCycle(target.endTime); + option->UseStartEndCycle = true; + } + ExtractedIonChromatogram^ xic = msExperiment->GetExtractedIonChromatogram(option); ToBinaryData(xic->GetActualXValues(), times); @@ -628,18 +638,10 @@ void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const { + basePeakY = getSIC(index, times, intensities); + try { - if (index >= transitionCount) - throw std::out_of_range("[Experiment::getSIC()] index " + lexical_cast(index) + " out of range"); - - ExtractedIonChromatogramSettings^ option = gcnew ExtractedIonChromatogramSettings(index); - ExtractedIonChromatogram^ xic = msExperiment->GetExtractedIonChromatogram(option); - - ToBinaryData(xic->GetActualXValues(), times); - ToBinaryData(xic->GetActualYValues(), intensities); - - basePeakY = xic->MaximumYValue; basePeakX = 0; for (size_t i=0; i < intensities.size(); ++i) if (intensities[i] == basePeakY) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp index 2e6c301dbb..8d1ac7a305 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp @@ -190,7 +190,7 @@ struct PWIZ_API_DECL Experiment virtual size_t getSRMSize() const = 0; virtual void getSRM(size_t index, Target& target) const = 0; - virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const = 0; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const = 0; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const = 0; diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp index c4dc5c9f05..e94ebcacf8 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp @@ -128,7 +128,7 @@ struct Experiment2Impl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const; @@ -564,10 +564,11 @@ void Experiment2Impl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -void Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const { double x, y; getSIC(index, times, intensities, x, y); + return y; } void Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, From 489631bb2f9c405abed5ef4c5ee60b577bb67aa5 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Fri, 17 Feb 2023 14:01:54 -0500 Subject: [PATCH 05/14] - added ignoreScheduledLimitsForChromatograms flag for telling pwiz to try to get SIM/SRM chromatograms from the entire time range instead of within the scheduled limits; works around a bug(?) with Sciex WIFF where it records the wrong scheduled limits but the data is actually there if you tell it to ignore the limits (reported by Phillip and Celeste) --- pwiz/data/msdata/Reader.cpp | 2 ++ pwiz/data/msdata/Reader.hpp | 4 ++++ .../ABI/ChromatogramList_ABI.cpp | 4 ++-- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 18 ++++++++++++------ .../msrc/utility/vendor_api/ABI/WiffFile.hpp | 4 ++-- .../msrc/utility/vendor_api/ABI/WiffFile2.ipp | 10 +++++----- pwiz_tools/commandline/msconvert.cpp | 10 +++------- 7 files changed, 30 insertions(+), 22 deletions(-) diff --git a/pwiz/data/msdata/Reader.cpp b/pwiz/data/msdata/Reader.cpp index 577f073770..8ab14325e8 100755 --- a/pwiz/data/msdata/Reader.cpp +++ b/pwiz/data/msdata/Reader.cpp @@ -52,6 +52,7 @@ Reader::Config::Config() , sortAndJitter(false) , globalChromatogramsAreMs1Only(false) , ddaProcessing(false) + , ignoreScheduledLimitsForChromatograms(false) { } @@ -74,6 +75,7 @@ Reader::Config::Config(const Config& rhs) isolationMzAndMobilityFilter = rhs.isolationMzAndMobilityFilter; sortAndJitter = rhs.sortAndJitter; globalChromatogramsAreMs1Only = rhs.globalChromatogramsAreMs1Only; + ignoreScheduledLimitsForChromatograms = rhs.ignoreScheduledLimitsForChromatograms; } // default implementation; most Readers don't need to worry about multi-run input files diff --git a/pwiz/data/msdata/Reader.hpp b/pwiz/data/msdata/Reader.hpp index c119a305b7..8d7edd38b5 100755 --- a/pwiz/data/msdata/Reader.hpp +++ b/pwiz/data/msdata/Reader.hpp @@ -96,6 +96,10 @@ class PWIZ_API_DECL Reader // to the same precursor from the same survey scan, and lockmass-correcting the precursor mass (if the lockmass refiner is active). bool ddaProcessing; + /// when true, scheduled SIM/SRM chromatograms will try to get an XIC covering the entire range instead of just the scheduled range + /// (useful if the instrument recorded extra data outside the scheduled limits, currently only applicable to Sciex WIFF) + bool ignoreScheduledLimitsForChromatograms; + Config(); Config(const Config& rhs); }; diff --git a/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp b/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp index 55bf2b9f0a..1a18eb605b 100644 --- a/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp +++ b/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp @@ -251,7 +251,7 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D result->setTimeIntensityArrays(std::vector(), std::vector(), UO_minute, MS_number_of_detector_counts); pwiz::util::BinaryData times, intensities; - experiment->getSIC(ie.transition, times, intensities); + experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms); result->defaultArrayLength = times.size(); if (getBinaryData) @@ -290,7 +290,7 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D result->setTimeIntensityArrays(std::vector(), std::vector(), UO_minute, MS_number_of_detector_counts); pwiz::util::BinaryData times, intensities; - experiment->getSIC(ie.transition, times, intensities); + experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms); result->defaultArrayLength = times.size(); if (getBinaryData) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 0229ff78ab..559303242b 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -130,9 +130,9 @@ struct ExperimentImpl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const; + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const; virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const; virtual ScanType getScanType() const; @@ -609,7 +609,7 @@ void ExperimentImpl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const { try { @@ -620,7 +620,13 @@ double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& time getSRM(index, target); ExtractedIonChromatogramSettings^ option = gcnew ExtractedIonChromatogramSettings(index); - if (target.startTime != target.endTime) + if (ignoreScheduledLimits) + { + option->StartCycle = 0; + option->EndCycle = convertRetentionTimeToCycle(cycleTimes().back()); + option->UseStartEndCycle = true; + } + else if (target.startTime != target.endTime) { option->StartCycle = convertRetentionTimeToCycle(target.startTime); option->EndCycle = convertRetentionTimeToCycle(target.endTime); @@ -636,9 +642,9 @@ double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& time } void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const { - basePeakY = getSIC(index, times, intensities); + basePeakY = getSIC(index, times, intensities, ignoreScheduledLimits); try { diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp index 8d1ac7a305..38103b57f5 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp @@ -190,9 +190,9 @@ struct PWIZ_API_DECL Experiment virtual size_t getSRMSize() const = 0; virtual void getSRM(size_t index, Target& target) const = 0; - virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const = 0; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const = 0; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const = 0; + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const = 0; virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const = 0; virtual ScanType getScanType() const = 0; diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp index e94ebcacf8..5027ffa8aa 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp @@ -128,9 +128,9 @@ struct Experiment2Impl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const; + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const; virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const; virtual ScanType getScanType() const; @@ -564,15 +564,15 @@ void Experiment2Impl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const { double x, y; - getSIC(index, times, intensities, x, y); + getSIC(index, times, intensities, x, y, ignoreScheduledLimits); return y; } void Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const { try { diff --git a/pwiz_tools/commandline/msconvert.cpp b/pwiz_tools/commandline/msconvert.cpp index 6e6eac3622..6767280525 100644 --- a/pwiz_tools/commandline/msconvert.cpp +++ b/pwiz_tools/commandline/msconvert.cpp @@ -70,15 +70,8 @@ struct Config : public Reader::Config Config() : outputPath("."), verbose(false), merge(false) { - simAsSpectra = false; - srmAsSpectra = false; - combineIonMobilitySpectra = false; - ignoreCalibrationScans = false; - reportSonarBins = false; - unknownInstrumentIsError = true; stripLocationFromSourceFiles = false; stripVersionFromSoftware = false; - ddaProcessing = false; } string outputFilename(const string& inputFilename, const MSData& inputMSData) const; @@ -344,6 +337,9 @@ Config parseCommandLine(int argc, char** argv) ("ignoreCalibrationScans", po::value(&config.ignoreCalibrationScans)->zero_tokens(), ": do not process calibration scans (currently only applies to Waters lockmass function)") + ("ignoreScheduledLimitsForChromatograms", + po::value(&config.ignoreScheduledLimitsForChromatograms)->zero_tokens(), + ": scheduled SIM/SRM chromatograms will try to get an XIC covering the entire run time instead of just the scheduled limits") ("acceptZeroLengthSpectra", po::value(&config.acceptZeroLengthSpectra)->zero_tokens(), ": some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file") From afad3157f399281617645b2a239355a059ce1500 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Thu, 2 Mar 2023 16:16:16 -0500 Subject: [PATCH 06/14] * added CLI binding for ignoreScheduledLimitsForChromatograms --- pwiz/utility/bindings/CLI/msdata/Reader.cpp | 1 + pwiz/utility/bindings/CLI/msdata/Reader.hpp | 37 +++++++++++++++++++++ 2 files changed, 38 insertions(+) diff --git a/pwiz/utility/bindings/CLI/msdata/Reader.cpp b/pwiz/utility/bindings/CLI/msdata/Reader.cpp index 4cb643fcd3..eab2e27632 100644 --- a/pwiz/utility/bindings/CLI/msdata/Reader.cpp +++ b/pwiz/utility/bindings/CLI/msdata/Reader.cpp @@ -86,6 +86,7 @@ static void copyReaderConfig(pwiz::msdata::Reader::Config& config, ReaderConfig^ config.sortAndJitter = readerConfig->sortAndJitter; config.globalChromatogramsAreMs1Only = readerConfig->globalChromatogramsAreMs1Only; config.ddaProcessing = readerConfig->ddaProcessing; + config.ignoreScheduledLimitsForChromatograms = readerConfig->ignoreScheduledLimitsForChromatograms; if (readerConfig->isolationMzAndMobilityFilter != nullptr) for each (MzMobilityWindow^ filter in readerConfig->isolationMzAndMobilityFilter) diff --git a/pwiz/utility/bindings/CLI/msdata/Reader.hpp b/pwiz/utility/bindings/CLI/msdata/Reader.hpp index 2f69d3de7e..de8157474a 100644 --- a/pwiz/utility/bindings/CLI/msdata/Reader.hpp +++ b/pwiz/utility/bindings/CLI/msdata/Reader.hpp @@ -67,54 +67,90 @@ public ref class ReaderConfig { public: + /// /// return Selected Ion Monitoring as spectra + /// bool simAsSpectra; + /// /// return Selected Reaction Monitoring as spectra + /// bool srmAsSpectra; + /// /// when true, allows for skipping 0 length checks (and thus skip re-reading data for ABI) + /// bool acceptZeroLengthSpectra; + /// /// when true, allows certain vendor readers to produce profile data without zero intensity samples flanking each peak profile + /// bool ignoreZeroIntensityPoints; + /// /// when true, all drift bins/scans in a frame/block are written in combined form instead of as individual spectra + /// bool combineIonMobilitySpectra; + /// // when true, scans with only calibration data will be ignored (currently Waters lockmass only) + /// bool ignoreCalibrationScans; + /// /// when true, Waters SONAR data populates "drift" information with bin number instead of pseudo ion mobility values + /// bool reportSonarBins; + /// /// when true, if a reader cannot identify an instrument, an exception will be thrown asking users to report it + /// bool unknownInstrumentIsError; + /// /// when true, if a reader does not know what time zone was used to record a time, it will assume the time refers to the host's local time; /// when false, the reader will treat times with unknown time zone as UTC + /// bool adjustUnknownTimeZonesToHostTimeZone; + /// /// when nonzero, if reader can enumerate only spectra of ms level, it will (currently only supported by Bruker TDF) + /// int preferOnlyMsLevel; + /// /// when true, MS2 spectra without precursor/isolation information will be included in the output (currently only affects Bruker PASEF data) + /// bool allowMsMsWithoutPrecursor; + /// /// temporary(?) variable to avoid needing to regenerate Bruker test data + /// bool sortAndJitter; + /// /// when non-empty, only scans from precursors matching one of the included m/z and/or mobility windows will be enumerated; MS1 scans are affected only by the mobility filter + /// System::Collections::Generic::IList^ isolationMzAndMobilityFilter; + /// /// when true, global TIC and BPC chromatograms consist of only MS1 spectra (thus the number of time points cannot be assumed to be equal to the number of spectra) + /// bool globalChromatogramsAreMs1Only; + /// // When true, vendor-specific DDA processing is enabled. For Waters data, this involves combining MS2 scans which refer // to the same precursor from the same survey scan, and lockmass-correcting the precursor mass (if the lockmass refiner is active). + /// bool ddaProcessing; + /// + /// when true, scheduled SIM/SRM chromatograms will try to get an XIC covering the entire range instead of just the scheduled range + /// (useful if the instrument recorded extra data outside the scheduled limits, currently only applicable to Sciex WIFF) + /// + bool ignoreScheduledLimitsForChromatograms; + ReaderConfig() : simAsSpectra(false) , srmAsSpectra(false) @@ -130,6 +166,7 @@ public ref class ReaderConfig , sortAndJitter(false) , globalChromatogramsAreMs1Only(false) , ddaProcessing(false) + , ignoreScheduledLimitsForChromatograms(false) { } }; From cf5313402a799228ff09e90ccb1ce6c1bd3ad10c Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Wed, 8 Feb 2023 11:41:54 -0500 Subject: [PATCH 07/14] - added automatic doubling of SIM/SRM RTWindows if a WIFF file was collected by SCIEX OS version less than 3.1 (reported by Phillip) * removed very old conditional code for .NET < 4 --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 52 +++++++++++-------- 1 file changed, 29 insertions(+), 23 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 118873572f..6b7b437ff0 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -36,6 +36,7 @@ #include #include #include +#include #pragma managed #include "pwiz/utility/misc/cpp_cli_utilities.hpp" @@ -48,10 +49,8 @@ using namespace Clearcore2::Data::AnalystDataProvider; using namespace Clearcore2::Data::Client; using namespace Clearcore2::Data::DataAccess; using namespace Clearcore2::Data::DataAccess::SampleData; - -#if __CLR_VER > 40000000 // .NET 4 using namespace Clearcore2::RawXYProcessing; -#endif +namespace bxp = boost::xpressive; // peak areas from Sciex are very small values relative to peak heights; // multiplying them by this scaling factor makes them more comparable @@ -147,6 +146,7 @@ struct ExperimentImpl : public Experiment const WiffFileImpl* wifffile_; gcroot msExperiment; int sample, period, experiment; + bool hasHalfSizeRTWindow; ExperimentType experimentType; size_t simCount; @@ -203,10 +203,7 @@ struct SpectrumImpl : public Spectrum ExperimentImplPtr experiment; gcroot spectrumInfo; mutable gcroot spectrum; - -#if __CLR_VER > 40000000 // .NET 4 mutable gcroot^> peakList; -#endif int cycle; @@ -241,11 +238,7 @@ WiffFileImpl::WiffFileImpl(const string& wiffpath) { try { -/*#if __CLR_VER > 40000000 // .NET 4 - Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; -#else - Licenser::LicenseKey = ABI_BETA_LICENSE_KEY; -#endif*/ + //Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; provider = DataProviderFactory::CreateDataProvider("", true); //provider = gcnew AnalystWiffDataProvider(); @@ -439,6 +432,25 @@ ExperimentImpl::ExperimentImpl(const WiffFileImpl* wifffile, int sample, int per transitionCount = msExperiment->Details->MassRangeInfo->Length; else if (experimentType == SIM) simCount = msExperiment->Details->MassRangeInfo->Length; + + hasHalfSizeRTWindow = false; + try + { + auto softwareVersion = ToStdString(wifffile_->batch->GetSample(sample)->Details->SoftwareVersion); + bxp::sregex sciexOsVersionRegex = bxp::sregex::compile(R"(SCIEX OS (\d+)\.(\d+))"); + + bxp::smatch match; + if (bxp::regex_match(softwareVersion, match, sciexOsVersionRegex)) + { + int major = lexical_cast(match[1].str()); + int minor = lexical_cast(match[2].str()); + hasHalfSizeRTWindow = !(major >= 3 && minor >= 1); // currently assumed present in SCIEX OS lower than v3.1 + } + } + catch (Exception^) + { + // ignore read past end of stream: no version details? probably acquired with Analyst? + } } CATCH_AND_FORWARD } @@ -523,11 +535,12 @@ void ExperimentImpl::getSIM(size_t index, Target& target) const SIMMassRange^ transition = (SIMMassRange^) msExperiment->Details->MassRangeInfo[index]; + double rtWindowMultiplier = hasHalfSizeRTWindow ? 1 : 0.5; target.type = TargetType_SIM; target.Q1 = transition->Mass; target.dwellTime = transition->DwellTime; - target.startTime = transition->ExpectedRT - transition->RTWindow / 2; - target.endTime = transition->ExpectedRT + transition->RTWindow / 2; + target.startTime = transition->ExpectedRT - transition->RTWindow * rtWindowMultiplier; + target.endTime = transition->ExpectedRT + transition->RTWindow * rtWindowMultiplier; target.compoundID = ToStdString(transition->Name); auto parameters = transition->CompoundDepParameters; @@ -561,12 +574,13 @@ void ExperimentImpl::getSRM(size_t index, Target& target) const MRMMassRange^ transition = (MRMMassRange^) msExperiment->Details->MassRangeInfo[index]; + double rtWindowMultiplier = hasHalfSizeRTWindow ? 1 : 0.5; target.type = TargetType_SRM; target.Q1 = transition->Q1Mass; target.Q3 = transition->Q3Mass; target.dwellTime = transition->DwellTime; - target.startTime = transition->ExpectedRT - transition->RTWindow; - target.endTime = transition->ExpectedRT + transition->RTWindow; + target.startTime = transition->ExpectedRT - transition->RTWindow * rtWindowMultiplier; + target.endTime = transition->ExpectedRT + transition->RTWindow * rtWindowMultiplier; target.compoundID = ToStdString(transition->Name); auto parameters = transition->CompoundDepParameters; @@ -768,23 +782,19 @@ size_t SpectrumImpl::getDataSize(bool doCentroid, bool ignoreZeroIntensityPoints if (experimentType == MRM || experimentType == SIM) return experiment->msExperiment->Details->MassRangeInfo->Length; -#if __CLR_VER > 40000000 // .NET 4 if (doCentroid) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); return (size_t) peakList->Length; } else -#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); -#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); -#endif } return (size_t) spectrum->NumDataPoints; } @@ -797,7 +807,6 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, { try { -#if __CLR_VER > 40000000 // .NET 4 if (doCentroid && pointsAreContinuous) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); @@ -812,15 +821,12 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, } } else -#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); -#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); -#endif } // XValues are not m/z values for MRM and SIM experiments From 43e925f86e1e5851b848027b5d376b4d98d929e3 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Wed, 8 Feb 2023 16:14:46 -0500 Subject: [PATCH 08/14] * restored .NET < 4 checks to see if that has something to do with installer test failures --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 21 +++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 6b7b437ff0..baf798772d 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -49,8 +49,10 @@ using namespace Clearcore2::Data::AnalystDataProvider; using namespace Clearcore2::Data::Client; using namespace Clearcore2::Data::DataAccess; using namespace Clearcore2::Data::DataAccess::SampleData; + +#if __CLR_VER > 40000000 // .NET 4 using namespace Clearcore2::RawXYProcessing; -namespace bxp = boost::xpressive; +#endif // peak areas from Sciex are very small values relative to peak heights; // multiplying them by this scaling factor makes them more comparable @@ -203,7 +205,10 @@ struct SpectrumImpl : public Spectrum ExperimentImplPtr experiment; gcroot spectrumInfo; mutable gcroot spectrum; + +#if __CLR_VER > 40000000 // .NET 4 mutable gcroot^> peakList; +#endif int cycle; @@ -238,7 +243,11 @@ WiffFileImpl::WiffFileImpl(const string& wiffpath) { try { - //Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; +/*#if __CLR_VER > 40000000 // .NET 4 + Clearcore2::Licensing::LicenseKeys::Keys = gcnew array {ABI_BETA_LICENSE_KEY}; +#else + Licenser::LicenseKey = ABI_BETA_LICENSE_KEY; +#endif*/ provider = DataProviderFactory::CreateDataProvider("", true); //provider = gcnew AnalystWiffDataProvider(); @@ -782,19 +791,23 @@ size_t SpectrumImpl::getDataSize(bool doCentroid, bool ignoreZeroIntensityPoints if (experimentType == MRM || experimentType == SIM) return experiment->msExperiment->Details->MassRangeInfo->Length; +#if __CLR_VER > 40000000 // .NET 4 if (doCentroid) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); return (size_t) peakList->Length; } else +#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); +#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); +#endif } return (size_t) spectrum->NumDataPoints; } @@ -807,6 +820,7 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, { try { +#if __CLR_VER > 40000000 // .NET 4 if (doCentroid && pointsAreContinuous) { if ((cli::array^) peakList == nullptr) peakList = experiment->msExperiment->GetPeakArray(cycle-1); @@ -821,12 +835,15 @@ void SpectrumImpl::getData(bool doCentroid, pwiz::util::BinaryData& mz, } } else +#endif { if ((MassSpectrum^) spectrum == nullptr) { spectrum = experiment->msExperiment->GetMassSpectrum(cycle-1); +#if __CLR_VER > 40000000 // the .NET 4 version has an efficient way to add zeros if (!ignoreZeroIntensityPoints && pointsAreContinuous) experiment->msExperiment->AddZeros((MassSpectrum^) spectrum, 1); +#endif } // XValues are not m/z values for MRM and SIM experiments From 7a9ff67ca7c86d26126c89b674cd6e2c95303b9e Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Thu, 9 Feb 2023 16:16:08 -0500 Subject: [PATCH 09/14] * switched from xpressive to .NET Regex --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index baf798772d..23eb606892 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -36,14 +36,15 @@ #include #include #include -#include #pragma managed #include "pwiz/utility/misc/cpp_cli_utilities.hpp" #include +#using #using using namespace pwiz::util; using namespace System; +using namespace System::Text::RegularExpressions; using namespace Clearcore2::Data; using namespace Clearcore2::Data::AnalystDataProvider; using namespace Clearcore2::Data::Client; @@ -445,15 +446,17 @@ ExperimentImpl::ExperimentImpl(const WiffFileImpl* wifffile, int sample, int per hasHalfSizeRTWindow = false; try { - auto softwareVersion = ToStdString(wifffile_->batch->GetSample(sample)->Details->SoftwareVersion); - bxp::sregex sciexOsVersionRegex = bxp::sregex::compile(R"(SCIEX OS (\d+)\.(\d+))"); + auto softwareVersion = wifffile_->batch->GetSample(sample)->Details->SoftwareVersion; + auto sciexOsVersionRegex = gcnew Regex(R"(SCIEX OS (\d+)\.(\d+))"); - bxp::smatch match; - if (bxp::regex_match(softwareVersion, match, sciexOsVersionRegex)) + auto match = sciexOsVersionRegex->Match(softwareVersion); + if (match->Success) { - int major = lexical_cast(match[1].str()); - int minor = lexical_cast(match[2].str()); + int major = Convert::ToInt32(match->Groups[1]->Value); + int minor = Convert::ToInt32(match->Groups[2]->Value); hasHalfSizeRTWindow = !(major >= 3 && minor >= 1); // currently assumed present in SCIEX OS lower than v3.1 + //if (hasHalfSizeRTWindow) + // Console::Error->WriteLine("NOTE: data from " + softwareVersion + " has bugged half-width RTWindows"); } } catch (Exception^) From 1df08c641ca96ac1d22dceadb3332dbcb4ed230f Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Fri, 10 Feb 2023 11:25:02 -0500 Subject: [PATCH 10/14] - added start/end cycle override for SIM/SRM XICs from WIFF --- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 28 ++++++++++--------- .../msrc/utility/vendor_api/ABI/WiffFile.hpp | 2 +- .../msrc/utility/vendor_api/ABI/WiffFile2.ipp | 5 ++-- 3 files changed, 19 insertions(+), 16 deletions(-) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 23eb606892..0229ff78ab 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -130,7 +130,7 @@ struct ExperimentImpl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const; @@ -609,14 +609,24 @@ void ExperimentImpl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const { try { if (index >= transitionCount+simCount) - throw std::out_of_range("[Experiment::getSIC()] index out of range"); + throw std::out_of_range("[Experiment::getSIC()] index " + lexical_cast(index) + " out of range"); + + Target target; + getSRM(index, target); ExtractedIonChromatogramSettings^ option = gcnew ExtractedIonChromatogramSettings(index); + if (target.startTime != target.endTime) + { + option->StartCycle = convertRetentionTimeToCycle(target.startTime); + option->EndCycle = convertRetentionTimeToCycle(target.endTime); + option->UseStartEndCycle = true; + } + ExtractedIonChromatogram^ xic = msExperiment->GetExtractedIonChromatogram(option); ToBinaryData(xic->GetActualXValues(), times); @@ -628,18 +638,10 @@ void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const { + basePeakY = getSIC(index, times, intensities); + try { - if (index >= transitionCount) - throw std::out_of_range("[Experiment::getSIC()] index " + lexical_cast(index) + " out of range"); - - ExtractedIonChromatogramSettings^ option = gcnew ExtractedIonChromatogramSettings(index); - ExtractedIonChromatogram^ xic = msExperiment->GetExtractedIonChromatogram(option); - - ToBinaryData(xic->GetActualXValues(), times); - ToBinaryData(xic->GetActualYValues(), intensities); - - basePeakY = xic->MaximumYValue; basePeakX = 0; for (size_t i=0; i < intensities.size(); ++i) if (intensities[i] == basePeakY) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp index 2e6c301dbb..8d1ac7a305 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp @@ -190,7 +190,7 @@ struct PWIZ_API_DECL Experiment virtual size_t getSRMSize() const = 0; virtual void getSRM(size_t index, Target& target) const = 0; - virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const = 0; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const = 0; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const = 0; diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp index 3de57c4164..723715fdc8 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp @@ -130,7 +130,7 @@ struct Experiment2Impl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, double& basePeakX, double& basePeakY) const; @@ -568,10 +568,11 @@ void Experiment2Impl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -void Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const { double x, y; getSIC(index, times, intensities, x, y); + return y; } void Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, From 163826c547a94abf2054532b4d72c27b13e5af9e Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Fri, 17 Feb 2023 14:01:54 -0500 Subject: [PATCH 11/14] - added ignoreScheduledLimitsForChromatograms flag for telling pwiz to try to get SIM/SRM chromatograms from the entire time range instead of within the scheduled limits; works around a bug(?) with Sciex WIFF where it records the wrong scheduled limits but the data is actually there if you tell it to ignore the limits (reported by Phillip and Celeste) --- pwiz/data/msdata/Reader.cpp | 2 ++ pwiz/data/msdata/Reader.hpp | 4 ++++ .../ABI/ChromatogramList_ABI.cpp | 4 ++-- .../msrc/utility/vendor_api/ABI/WiffFile.cpp | 18 ++++++++++++------ .../msrc/utility/vendor_api/ABI/WiffFile.hpp | 4 ++-- .../msrc/utility/vendor_api/ABI/WiffFile2.ipp | 10 +++++----- pwiz_tools/commandline/msconvert.cpp | 10 +++------- 7 files changed, 30 insertions(+), 22 deletions(-) diff --git a/pwiz/data/msdata/Reader.cpp b/pwiz/data/msdata/Reader.cpp index 577f073770..8ab14325e8 100755 --- a/pwiz/data/msdata/Reader.cpp +++ b/pwiz/data/msdata/Reader.cpp @@ -52,6 +52,7 @@ Reader::Config::Config() , sortAndJitter(false) , globalChromatogramsAreMs1Only(false) , ddaProcessing(false) + , ignoreScheduledLimitsForChromatograms(false) { } @@ -74,6 +75,7 @@ Reader::Config::Config(const Config& rhs) isolationMzAndMobilityFilter = rhs.isolationMzAndMobilityFilter; sortAndJitter = rhs.sortAndJitter; globalChromatogramsAreMs1Only = rhs.globalChromatogramsAreMs1Only; + ignoreScheduledLimitsForChromatograms = rhs.ignoreScheduledLimitsForChromatograms; } // default implementation; most Readers don't need to worry about multi-run input files diff --git a/pwiz/data/msdata/Reader.hpp b/pwiz/data/msdata/Reader.hpp index c119a305b7..8d7edd38b5 100755 --- a/pwiz/data/msdata/Reader.hpp +++ b/pwiz/data/msdata/Reader.hpp @@ -96,6 +96,10 @@ class PWIZ_API_DECL Reader // to the same precursor from the same survey scan, and lockmass-correcting the precursor mass (if the lockmass refiner is active). bool ddaProcessing; + /// when true, scheduled SIM/SRM chromatograms will try to get an XIC covering the entire range instead of just the scheduled range + /// (useful if the instrument recorded extra data outside the scheduled limits, currently only applicable to Sciex WIFF) + bool ignoreScheduledLimitsForChromatograms; + Config(); Config(const Config& rhs); }; diff --git a/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp b/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp index 55bf2b9f0a..1a18eb605b 100644 --- a/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp +++ b/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp @@ -251,7 +251,7 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D result->setTimeIntensityArrays(std::vector(), std::vector(), UO_minute, MS_number_of_detector_counts); pwiz::util::BinaryData times, intensities; - experiment->getSIC(ie.transition, times, intensities); + experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms); result->defaultArrayLength = times.size(); if (getBinaryData) @@ -290,7 +290,7 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D result->setTimeIntensityArrays(std::vector(), std::vector(), UO_minute, MS_number_of_detector_counts); pwiz::util::BinaryData times, intensities; - experiment->getSIC(ie.transition, times, intensities); + experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms); result->defaultArrayLength = times.size(); if (getBinaryData) diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp index 0229ff78ab..559303242b 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp @@ -130,9 +130,9 @@ struct ExperimentImpl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const; + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const; virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const; virtual ScanType getScanType() const; @@ -609,7 +609,7 @@ void ExperimentImpl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const { try { @@ -620,7 +620,13 @@ double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& time getSRM(index, target); ExtractedIonChromatogramSettings^ option = gcnew ExtractedIonChromatogramSettings(index); - if (target.startTime != target.endTime) + if (ignoreScheduledLimits) + { + option->StartCycle = 0; + option->EndCycle = convertRetentionTimeToCycle(cycleTimes().back()); + option->UseStartEndCycle = true; + } + else if (target.startTime != target.endTime) { option->StartCycle = convertRetentionTimeToCycle(target.startTime); option->EndCycle = convertRetentionTimeToCycle(target.endTime); @@ -636,9 +642,9 @@ double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& time } void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const { - basePeakY = getSIC(index, times, intensities); + basePeakY = getSIC(index, times, intensities, ignoreScheduledLimits); try { diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp index 8d1ac7a305..38103b57f5 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp @@ -190,9 +190,9 @@ struct PWIZ_API_DECL Experiment virtual size_t getSRMSize() const = 0; virtual void getSRM(size_t index, Target& target) const = 0; - virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const = 0; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const = 0; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const = 0; + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const = 0; virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const = 0; virtual ScanType getScanType() const = 0; diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp index 723715fdc8..7cb9a45b8f 100644 --- a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp +++ b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp @@ -130,9 +130,9 @@ struct Experiment2Impl : public Experiment virtual size_t getSRMSize() const; virtual void getSRM(size_t index, Target& target) const; - virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const; + virtual double getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const; virtual void getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const; + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const; virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const; virtual ScanType getScanType() const; @@ -568,15 +568,15 @@ void Experiment2Impl::getSRM(size_t index, Target& target) const CATCH_AND_FORWARD } -double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities) const +double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, bool ignoreScheduledLimits) const { double x, y; - getSIC(index, times, intensities, x, y); + getSIC(index, times, intensities, x, y, ignoreScheduledLimits); return y; } void Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData& times, pwiz::util::BinaryData& intensities, - double& basePeakX, double& basePeakY) const + double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const { try { diff --git a/pwiz_tools/commandline/msconvert.cpp b/pwiz_tools/commandline/msconvert.cpp index 2945ffca54..d04fdf54e1 100644 --- a/pwiz_tools/commandline/msconvert.cpp +++ b/pwiz_tools/commandline/msconvert.cpp @@ -71,15 +71,8 @@ struct Config : public Reader::Config Config() : outputPath("."), verbose(false), merge(false) { - simAsSpectra = false; - srmAsSpectra = false; - combineIonMobilitySpectra = false; - ignoreCalibrationScans = false; - reportSonarBins = false; - unknownInstrumentIsError = true; stripLocationFromSourceFiles = false; stripVersionFromSoftware = false; - ddaProcessing = false; } string outputFilename(const string& inputFilename, const MSData& inputMSData) const; @@ -345,6 +338,9 @@ Config parseCommandLine(int argc, char** argv) ("ignoreCalibrationScans", po::value(&config.ignoreCalibrationScans)->zero_tokens(), ": do not process calibration scans (currently only applies to Waters lockmass function)") + ("ignoreScheduledLimitsForChromatograms", + po::value(&config.ignoreScheduledLimitsForChromatograms)->zero_tokens(), + ": scheduled SIM/SRM chromatograms will try to get an XIC covering the entire run time instead of just the scheduled limits") ("acceptZeroLengthSpectra", po::value(&config.acceptZeroLengthSpectra)->zero_tokens(), ": some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file") From e238df0184aaf56e6ee2f92b03af69c3efd114cc Mon Sep 17 00:00:00 2001 From: Nicholas Shulman Date: Tue, 14 Nov 2023 15:11:41 -0800 Subject: [PATCH 12/14] Add "ignoreScheduledLimitsForChromatograms" to CLI binding ReaderConfig Set "ignoreScheduledLimitsForChromatograms" to true in MsDataFileImpl constructor. Update expected values for "TestSrmTutorialLegacy" and "TestPeakPickingTutorial" --- pwiz/utility/bindings/CLI/msdata/Reader.cpp | 1 + pwiz/utility/bindings/CLI/msdata/Reader.hpp | 5 + .../ProteowizardWrapper/MsDataFileImpl.cs | 3 +- .../TestTutorial/PeakPickingTutorialTest.cs | 4 +- .../en/TestPeakPickingTutorial.log | 144 +++++++++--------- .../en/TestSrmTutorialLegacy.log | 4 +- .../fr/TestPeakPickingTutorial.log | 144 +++++++++--------- .../fr/TestSrmTutorialLegacy.log | 4 +- .../ja/TestPeakPickingTutorial.log | 144 +++++++++--------- .../ja/TestSrmTutorialLegacy.log | 4 +- .../tr/TestPeakPickingTutorial.log | 144 +++++++++--------- .../tr/TestSrmTutorialLegacy.log | 4 +- .../zh/TestPeakPickingTutorial.log | 144 +++++++++--------- .../zh/TestSrmTutorialLegacy.log | 4 +- 14 files changed, 380 insertions(+), 373 deletions(-) diff --git a/pwiz/utility/bindings/CLI/msdata/Reader.cpp b/pwiz/utility/bindings/CLI/msdata/Reader.cpp index 4cb643fcd3..eab2e27632 100644 --- a/pwiz/utility/bindings/CLI/msdata/Reader.cpp +++ b/pwiz/utility/bindings/CLI/msdata/Reader.cpp @@ -86,6 +86,7 @@ static void copyReaderConfig(pwiz::msdata::Reader::Config& config, ReaderConfig^ config.sortAndJitter = readerConfig->sortAndJitter; config.globalChromatogramsAreMs1Only = readerConfig->globalChromatogramsAreMs1Only; config.ddaProcessing = readerConfig->ddaProcessing; + config.ignoreScheduledLimitsForChromatograms = readerConfig->ignoreScheduledLimitsForChromatograms; if (readerConfig->isolationMzAndMobilityFilter != nullptr) for each (MzMobilityWindow^ filter in readerConfig->isolationMzAndMobilityFilter) diff --git a/pwiz/utility/bindings/CLI/msdata/Reader.hpp b/pwiz/utility/bindings/CLI/msdata/Reader.hpp index 2f69d3de7e..407e217563 100644 --- a/pwiz/utility/bindings/CLI/msdata/Reader.hpp +++ b/pwiz/utility/bindings/CLI/msdata/Reader.hpp @@ -115,6 +115,10 @@ public ref class ReaderConfig // to the same precursor from the same survey scan, and lockmass-correcting the precursor mass (if the lockmass refiner is active). bool ddaProcessing; + /// when true, scheduled SIM/SRM chromatograms will try to get an XIC covering the entire range instead of just the scheduled range + /// (useful if the instrument recorded extra data outside the scheduled limits, currently only applicable to Sciex WIFF) + bool ignoreScheduledLimitsForChromatograms; + ReaderConfig() : simAsSpectra(false) , srmAsSpectra(false) @@ -130,6 +134,7 @@ public ref class ReaderConfig , sortAndJitter(false) , globalChromatogramsAreMs1Only(false) , ddaProcessing(false) + , ignoreScheduledLimitsForChromatograms(false) { } }; diff --git a/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs b/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs index f61aa7d74e..a5a26f1acb 100644 --- a/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs +++ b/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs @@ -193,7 +193,8 @@ public MsDataFileImpl(string path, int sampleIndex = 0, LockMassParameters lockm combineIonMobilitySpectra = !ForceUncombinedIonMobility && combineIonMobilitySpectra, ignoreCalibrationScans = true, // For Waters, we don't need to hear about lockmass values reportSonarBins = true, // For Waters SONAR data, report bin number instead of false drift time - globalChromatogramsAreMs1Only = true + globalChromatogramsAreMs1Only = true, + ignoreScheduledLimitsForChromatograms = true }; _lockmassParameters = lockmassParameters; FULL_READER_LIST.read(path, _msDataFile, sampleIndex, _config); diff --git a/pwiz_tools/Skyline/TestTutorial/PeakPickingTutorialTest.cs b/pwiz_tools/Skyline/TestTutorial/PeakPickingTutorialTest.cs index b6f569c9df..a37a426e74 100644 --- a/pwiz_tools/Skyline/TestTutorial/PeakPickingTutorialTest.cs +++ b/pwiz_tools/Skyline/TestTutorial/PeakPickingTutorialTest.cs @@ -96,7 +96,7 @@ private string GetTestPath(string relativePath) private readonly string[] EXPECTED_COEFFICIENTS = { - "-0.0783|-0.7492|2.2424|1.2062|0.0331|0.1515|0.1767| null |0.4983|6.3997|-0.0482|0.5476|0.6281| null | null | null | null | null ", + "-0.1095|-0.7689|1.9147|0.9647|0.0265|0.1822|0.2229| null |0.5529|6.5433|-0.0357|0.5285|0.6585| null | null | null | null | null ", "0.2900| null | null |5.9842|-0.0624|0.6681|0.7968| null | null | null | null | null | null | null | null | null | null | null ", }; @@ -193,7 +193,7 @@ protected override void DoTest() var editDlg = ShowDialog(reintegrateDlg.AddPeakScoringModel); RunUI(() => editDlg.TrainModel()); PauseForScreenShot("Edit Peak Scoring Model form trained model", 6); - RunUI(() => Assert.AreEqual(0.5992, editDlg.PeakCalculatorsGrid.Items[3].PercentContribution ?? 0, 0.005)); + RunUI(() => Assert.AreEqual(0.5893, editDlg.PeakCalculatorsGrid.Items[3].PercentContribution ?? 0, 0.005)); RunUI(() => editDlg.SelectedGraphTab = 2); PauseForScreenShot("Edit Peak Scoring Model form p value graph metafile", 7); diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestPeakPickingTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestPeakPickingTutorial.log index db39e71c33..1c7e35eeb8 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestPeakPickingTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestPeakPickingTutorial.log @@ -66,18 +66,18 @@ Summary : Reintegrated peaks using "test1" All Info : Reintegrated peaks using "test1" Reintegrate > Peak scoring model is "test1" -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0.078328345434545", Percentage Contribution = "-0.021" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0.74923684676032", Percentage Contribution = "0.066" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "2.24238344148558", Percentage Contribution = "0.081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "1.20618462186508", Percentage Contribution = "0.081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0.0330641179011537", Percentage Contribution = "-0.031" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0.151546153152723", Percentage Contribution = "0.05" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0.176740916361492", Percentage Contribution = "0.042" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0.498299821042048", Percentage Contribution = "0.02" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6.39974546904101", Percentage Contribution = "0.4" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0.0482245507469112", Percentage Contribution = "0.04" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0.547648429894388", Percentage Contribution = "0.1" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0.628130085182893", Percentage Contribution = "0.172" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0.10947638732718", Percentage Contribution = "-0.03" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0.768944834471997", Percentage Contribution = "0.067" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "1.91473647678043", Percentage Contribution = "0.071" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "0.964673347739591", Percentage Contribution = "0.064" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0.0265095737294209", Percentage Contribution = "-0.023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0.182160151225063", Percentage Contribution = "0.062" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0.222902489204878", Percentage Contribution = "0.053" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0.552867011319634", Percentage Contribution = "0.023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6.54328045047817", Percentage Contribution = "0.406" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0.035670415865123", Percentage Contribution = "0.028" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0.528458461601712", Percentage Contribution = "0.099" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0.658504481008043", Percentage Contribution = "0.181" } Reintegrate > Peak scoring model > Use decoys is True Reintegrate > Peak scoring model > Uses second best peaks is False Reintegrate > Integrate all peaks is True @@ -88,63 +88,63 @@ Extra Info: Peak scoring model = "test1": [ { Score Name = "Intensity", - Weight = "-0.078328345434545", - Percentage Contribution = "-0.021" + Weight = "-0.10947638732718", + Percentage Contribution = "-0.03" }, { Score Name = "Retention time difference", - Weight = "-0.74923684676032", - Percentage Contribution = "0.066" + Weight = "-0.768944834471997", + Percentage Contribution = "0.067" }, { Score Name = "Library intensity dot-product", - Weight = "2.24238344148558", - Percentage Contribution = "0.081" + Weight = "1.91473647678043", + Percentage Contribution = "0.071" }, { Score Name = "Shape (weighted)", - Weight = "1.20618462186508", - Percentage Contribution = "0.081" + Weight = "0.964673347739591", + Percentage Contribution = "0.064" }, { Score Name = "Co-elution (weighted)", - Weight = "0.0330641179011537", - Percentage Contribution = "-0.031" + Weight = "0.0265095737294209", + Percentage Contribution = "-0.023" }, { Score Name = "Co-elution count", - Weight = "0.151546153152723", - Percentage Contribution = "0.05" + Weight = "0.182160151225063", + Percentage Contribution = "0.062" }, { Score Name = "Signal to noise", - Weight = "0.176740916361492", - Percentage Contribution = "0.042" + Weight = "0.222902489204878", + Percentage Contribution = "0.053" }, { Score Name = "Reference intensity dot-product", - Weight = "0.498299821042048", - Percentage Contribution = "0.02" + Weight = "0.552867011319634", + Percentage Contribution = "0.023" }, { Score Name = "Reference shape (weighted)", - Weight = "6.39974546904101", - Percentage Contribution = "0.4" + Weight = "6.54328045047817", + Percentage Contribution = "0.406" }, { Score Name = "Reference co-elution (weighted)", - Weight = "-0.0482245507469112", - Percentage Contribution = "0.04" + Weight = "-0.035670415865123", + Percentage Contribution = "0.028" }, { Score Name = "Reference co-elution count", - Weight = "0.547648429894388", - Percentage Contribution = "0.1" + Weight = "0.528458461601712", + Percentage Contribution = "0.099" }, { Score Name = "Standard Intensity", - Weight = "0.628130085182893", - Percentage Contribution = "0.172" + Weight = "0.658504481008043", + Percentage Contribution = "0.181" } ], Use decoys = True, @@ -158,18 +158,18 @@ Summary : Reintegrated peaks using "test1" All Info : Reintegrated peaks using "test1" Reintegrate > Peak scoring model is "test1" -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0.078328345434545", Percentage Contribution = "-0.021" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0.74923684676032", Percentage Contribution = "0.066" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "2.24238344148558", Percentage Contribution = "0.081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "1.20618462186508", Percentage Contribution = "0.081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0.0330641179011537", Percentage Contribution = "-0.031" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0.151546153152723", Percentage Contribution = "0.05" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0.176740916361492", Percentage Contribution = "0.042" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0.498299821042048", Percentage Contribution = "0.02" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6.39974546904101", Percentage Contribution = "0.4" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0.0482245507469112", Percentage Contribution = "0.04" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0.547648429894388", Percentage Contribution = "0.1" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0.628130085182893", Percentage Contribution = "0.172" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0.10947638732718", Percentage Contribution = "-0.03" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0.768944834471997", Percentage Contribution = "0.067" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "1.91473647678043", Percentage Contribution = "0.071" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "0.964673347739591", Percentage Contribution = "0.064" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0.0265095737294209", Percentage Contribution = "-0.023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0.182160151225063", Percentage Contribution = "0.062" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0.222902489204878", Percentage Contribution = "0.053" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0.552867011319634", Percentage Contribution = "0.023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6.54328045047817", Percentage Contribution = "0.406" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0.035670415865123", Percentage Contribution = "0.028" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0.528458461601712", Percentage Contribution = "0.099" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0.658504481008043", Percentage Contribution = "0.181" } Reintegrate > Peak scoring model > Use decoys is True Reintegrate > Peak scoring model > Uses second best peaks is False Reintegrate > Only integrate significant q values is True @@ -181,63 +181,63 @@ Extra Info: Peak scoring model = "test1": [ { Score Name = "Intensity", - Weight = "-0.078328345434545", - Percentage Contribution = "-0.021" + Weight = "-0.10947638732718", + Percentage Contribution = "-0.03" }, { Score Name = "Retention time difference", - Weight = "-0.74923684676032", - Percentage Contribution = "0.066" + Weight = "-0.768944834471997", + Percentage Contribution = "0.067" }, { Score Name = "Library intensity dot-product", - Weight = "2.24238344148558", - Percentage Contribution = "0.081" + Weight = "1.91473647678043", + Percentage Contribution = "0.071" }, { Score Name = "Shape (weighted)", - Weight = "1.20618462186508", - Percentage Contribution = "0.081" + Weight = "0.964673347739591", + Percentage Contribution = "0.064" }, { Score Name = "Co-elution (weighted)", - Weight = "0.0330641179011537", - Percentage Contribution = "-0.031" + Weight = "0.0265095737294209", + Percentage Contribution = "-0.023" }, { Score Name = "Co-elution count", - Weight = "0.151546153152723", - Percentage Contribution = "0.05" + Weight = "0.182160151225063", + Percentage Contribution = "0.062" }, { Score Name = "Signal to noise", - Weight = "0.176740916361492", - Percentage Contribution = "0.042" + Weight = "0.222902489204878", + Percentage Contribution = "0.053" }, { Score Name = "Reference intensity dot-product", - Weight = "0.498299821042048", - Percentage Contribution = "0.02" + Weight = "0.552867011319634", + Percentage Contribution = "0.023" }, { Score Name = "Reference shape (weighted)", - Weight = "6.39974546904101", - Percentage Contribution = "0.4" + Weight = "6.54328045047817", + Percentage Contribution = "0.406" }, { Score Name = "Reference co-elution (weighted)", - Weight = "-0.0482245507469112", - Percentage Contribution = "0.04" + Weight = "-0.035670415865123", + Percentage Contribution = "0.028" }, { Score Name = "Reference co-elution count", - Weight = "0.547648429894388", - Percentage Contribution = "0.1" + Weight = "0.528458461601712", + Percentage Contribution = "0.099" }, { Score Name = "Standard Intensity", - Weight = "0.628130085182893", - Percentage Contribution = "0.172" + Weight = "0.658504481008043", + Percentage Contribution = "0.181" } ], Use decoys = True, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestSrmTutorialLegacy.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestSrmTutorialLegacy.log index 8300635062..47d90a5f6b 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestSrmTutorialLegacy.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestSrmTutorialLegacy.log @@ -307,8 +307,8 @@ Summary : Settings > Transition Settings changed All Info : Transition Settings changed Settings > Transition Settings -- Prediction > Collision energy changed from "SCIEX" to "SRMcourse_20140211_Parameters_custom-CE-equation" -Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "2", Slope = "0.0369", Intercept = "3.9361" } -Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "3", Slope = "0.0208", Intercept = "9.0837" } +Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "2", Slope = "0.025", Intercept = "8.6852" } +Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "3", Slope = "0.046", Intercept = "-1.9754" } Settings > Transition Settings -- Instrument > Method match tolerance m/z changed from "0.055" to "0.01" Undo Redo : Managed results diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestPeakPickingTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestPeakPickingTutorial.log index 03bb4ca819..8f7bd0550f 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestPeakPickingTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestPeakPickingTutorial.log @@ -66,18 +66,18 @@ Summary : Reintegrated peaks using "test1" All Info : Reintegrated peaks using "test1" Reintegrate > Peak scoring model is "test1" -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,078328345434545", Percentage Contribution = "-0,021" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,74923684676032", Percentage Contribution = "0,066" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "2,24238344148558", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "1,20618462186508", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0330641179011537", Percentage Contribution = "-0,031" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,151546153152723", Percentage Contribution = "0,05" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,176740916361492", Percentage Contribution = "0,042" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,498299821042048", Percentage Contribution = "0,02" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,39974546904101", Percentage Contribution = "0,4" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,0482245507469112", Percentage Contribution = "0,04" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,547648429894388", Percentage Contribution = "0,1" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,628130085182893", Percentage Contribution = "0,172" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,10947638732718", Percentage Contribution = "-0,03" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,768944834471997", Percentage Contribution = "0,067" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "1,91473647678043", Percentage Contribution = "0,071" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "0,964673347739591", Percentage Contribution = "0,064" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0265095737294209", Percentage Contribution = "-0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,182160151225063", Percentage Contribution = "0,062" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,222902489204878", Percentage Contribution = "0,053" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,552867011319634", Percentage Contribution = "0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,54328045047817", Percentage Contribution = "0,406" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,035670415865123", Percentage Contribution = "0,028" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,528458461601712", Percentage Contribution = "0,099" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,658504481008043", Percentage Contribution = "0,181" } Reintegrate > Peak scoring model > Use decoys is True Reintegrate > Peak scoring model > Uses second best peaks is False Reintegrate > Integrate all peaks is True @@ -88,63 +88,63 @@ Extra Info: Peak scoring model = "test1": [ { Score Name = "Intensity", - Weight = "-0,078328345434545", - Percentage Contribution = "-0,021" + Weight = "-0,10947638732718", + Percentage Contribution = "-0,03" }, { Score Name = "Retention time difference", - Weight = "-0,74923684676032", - Percentage Contribution = "0,066" + Weight = "-0,768944834471997", + Percentage Contribution = "0,067" }, { Score Name = "Library intensity dot-product", - Weight = "2,24238344148558", - Percentage Contribution = "0,081" + Weight = "1,91473647678043", + Percentage Contribution = "0,071" }, { Score Name = "Shape (weighted)", - Weight = "1,20618462186508", - Percentage Contribution = "0,081" + Weight = "0,964673347739591", + Percentage Contribution = "0,064" }, { Score Name = "Co-elution (weighted)", - Weight = "0,0330641179011537", - Percentage Contribution = "-0,031" + Weight = "0,0265095737294209", + Percentage Contribution = "-0,023" }, { Score Name = "Co-elution count", - Weight = "0,151546153152723", - Percentage Contribution = "0,05" + Weight = "0,182160151225063", + Percentage Contribution = "0,062" }, { Score Name = "Signal to noise", - Weight = "0,176740916361492", - Percentage Contribution = "0,042" + Weight = "0,222902489204878", + Percentage Contribution = "0,053" }, { Score Name = "Reference intensity dot-product", - Weight = "0,498299821042048", - Percentage Contribution = "0,02" + Weight = "0,552867011319634", + Percentage Contribution = "0,023" }, { Score Name = "Reference shape (weighted)", - Weight = "6,39974546904101", - Percentage Contribution = "0,4" + Weight = "6,54328045047817", + Percentage Contribution = "0,406" }, { Score Name = "Reference co-elution (weighted)", - Weight = "-0,0482245507469112", - Percentage Contribution = "0,04" + Weight = "-0,035670415865123", + Percentage Contribution = "0,028" }, { Score Name = "Reference co-elution count", - Weight = "0,547648429894388", - Percentage Contribution = "0,1" + Weight = "0,528458461601712", + Percentage Contribution = "0,099" }, { Score Name = "Standard Intensity", - Weight = "0,628130085182893", - Percentage Contribution = "0,172" + Weight = "0,658504481008043", + Percentage Contribution = "0,181" } ], Use decoys = True, @@ -158,18 +158,18 @@ Summary : Reintegrated peaks using "test1" All Info : Reintegrated peaks using "test1" Reintegrate > Peak scoring model is "test1" -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,078328345434545", Percentage Contribution = "-0,021" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,74923684676032", Percentage Contribution = "0,066" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "2,24238344148558", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "1,20618462186508", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0330641179011537", Percentage Contribution = "-0,031" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,151546153152723", Percentage Contribution = "0,05" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,176740916361492", Percentage Contribution = "0,042" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,498299821042048", Percentage Contribution = "0,02" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,39974546904101", Percentage Contribution = "0,4" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,0482245507469112", Percentage Contribution = "0,04" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,547648429894388", Percentage Contribution = "0,1" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,628130085182893", Percentage Contribution = "0,172" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,10947638732718", Percentage Contribution = "-0,03" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,768944834471997", Percentage Contribution = "0,067" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "1,91473647678043", Percentage Contribution = "0,071" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "0,964673347739591", Percentage Contribution = "0,064" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0265095737294209", Percentage Contribution = "-0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,182160151225063", Percentage Contribution = "0,062" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,222902489204878", Percentage Contribution = "0,053" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,552867011319634", Percentage Contribution = "0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,54328045047817", Percentage Contribution = "0,406" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,035670415865123", Percentage Contribution = "0,028" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,528458461601712", Percentage Contribution = "0,099" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,658504481008043", Percentage Contribution = "0,181" } Reintegrate > Peak scoring model > Use decoys is True Reintegrate > Peak scoring model > Uses second best peaks is False Reintegrate > Only integrate significant q values is True @@ -181,63 +181,63 @@ Extra Info: Peak scoring model = "test1": [ { Score Name = "Intensity", - Weight = "-0,078328345434545", - Percentage Contribution = "-0,021" + Weight = "-0,10947638732718", + Percentage Contribution = "-0,03" }, { Score Name = "Retention time difference", - Weight = "-0,74923684676032", - Percentage Contribution = "0,066" + Weight = "-0,768944834471997", + Percentage Contribution = "0,067" }, { Score Name = "Library intensity dot-product", - Weight = "2,24238344148558", - Percentage Contribution = "0,081" + Weight = "1,91473647678043", + Percentage Contribution = "0,071" }, { Score Name = "Shape (weighted)", - Weight = "1,20618462186508", - Percentage Contribution = "0,081" + Weight = "0,964673347739591", + Percentage Contribution = "0,064" }, { Score Name = "Co-elution (weighted)", - Weight = "0,0330641179011537", - Percentage Contribution = "-0,031" + Weight = "0,0265095737294209", + Percentage Contribution = "-0,023" }, { Score Name = "Co-elution count", - Weight = "0,151546153152723", - Percentage Contribution = "0,05" + Weight = "0,182160151225063", + Percentage Contribution = "0,062" }, { Score Name = "Signal to noise", - Weight = "0,176740916361492", - Percentage Contribution = "0,042" + Weight = "0,222902489204878", + Percentage Contribution = "0,053" }, { Score Name = "Reference intensity dot-product", - Weight = "0,498299821042048", - Percentage Contribution = "0,02" + Weight = "0,552867011319634", + Percentage Contribution = "0,023" }, { Score Name = "Reference shape (weighted)", - Weight = "6,39974546904101", - Percentage Contribution = "0,4" + Weight = "6,54328045047817", + Percentage Contribution = "0,406" }, { Score Name = "Reference co-elution (weighted)", - Weight = "-0,0482245507469112", - Percentage Contribution = "0,04" + Weight = "-0,035670415865123", + Percentage Contribution = "0,028" }, { Score Name = "Reference co-elution count", - Weight = "0,547648429894388", - Percentage Contribution = "0,1" + Weight = "0,528458461601712", + Percentage Contribution = "0,099" }, { Score Name = "Standard Intensity", - Weight = "0,628130085182893", - Percentage Contribution = "0,172" + Weight = "0,658504481008043", + Percentage Contribution = "0,181" } ], Use decoys = True, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestSrmTutorialLegacy.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestSrmTutorialLegacy.log index c74dfe788b..cbb9ed8797 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestSrmTutorialLegacy.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestSrmTutorialLegacy.log @@ -307,8 +307,8 @@ Summary : Settings > Transition Settings changed All Info : Transition Settings changed Settings > Transition Settings -- Prediction > Collision energy changed from "SCIEX" to "SRMcourse_20140211_Parameters_custom-CE-equation" -Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "2", Slope = "0,0369", Intercept = "3,9361" } -Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "3", Slope = "0,0208", Intercept = "9,0837" } +Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "2", Slope = "0,025", Intercept = "8,6852" } +Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "3", Slope = "0,046", Intercept = "-1,9754" } Settings > Transition Settings -- Instrument > Method match tolerance m/z changed from "0,055" to "0,01" Undo Redo : Managed results diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestPeakPickingTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestPeakPickingTutorial.log index bb92e5f65a..5a8722adab 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestPeakPickingTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestPeakPickingTutorial.log @@ -66,18 +66,18 @@ Summary : 「test1」を使用してピークが再積分されました All Info : 「test1」を使用してピークが再積分されました 再積分>ピークスコアモデルは"test1"です -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "強度", 加重 = "-0.078328345434545", 貢献度 = "-0.021" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "保持時間の差異", 加重 = "-0.74923684676032", 貢献度 = "0.066" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "ライブラリ強度内積", 加重 = "2.24238344148558", 貢献度 = "0.081" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "形（加重）", 加重 = "1.20618462186508", 貢献度 = "0.081" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出（加重）", 加重 = "0.0330641179011537", 貢献度 = "-0.031" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出数", 加重 = "0.151546153152723", 貢献度 = "0.05" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "信号対ノイズ比", 加重 = "0.176740916361492", 貢献度 = "0.042" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照強度内積", 加重 = "0.498299821042048", 貢献度 = "0.02" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照形（加重）", 加重 = "6.39974546904101", 貢献度 = "0.4" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出（加重）", 加重 = "-0.0482245507469112", 貢献度 = "0.04" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出数", 加重 = "0.547648429894388", 貢献度 = "0.1" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "標準強度", 加重 = "0.628130085182893", 貢献度 = "0.172" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "強度", 加重 = "-0.10947638732718", 貢献度 = "-0.03" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "保持時間の差異", 加重 = "-0.768944834471997", 貢献度 = "0.067" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "ライブラリ強度内積", 加重 = "1.91473647678043", 貢献度 = "0.071" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "形（加重）", 加重 = "0.964673347739591", 貢献度 = "0.064" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出（加重）", 加重 = "0.0265095737294209", 貢献度 = "-0.023" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出数", 加重 = "0.182160151225063", 貢献度 = "0.062" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "信号対ノイズ比", 加重 = "0.222902489204878", 貢献度 = "0.053" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照強度内積", 加重 = "0.552867011319634", 貢献度 = "0.023" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照形（加重）", 加重 = "6.54328045047817", 貢献度 = "0.406" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出（加重）", 加重 = "-0.035670415865123", 貢献度 = "0.028" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出数", 加重 = "0.528458461601712", 貢献度 = "0.099" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "標準強度", 加重 = "0.658504481008043", 貢献度 = "0.181" }が含まれています 再積分>ピークスコアモデル>デコイを使用するは真です 再積分>ピークスコアモデル>2番目に良いピークを使用は偽です 再積分>すべてのピークを積分は真です @@ -88,63 +88,63 @@ Extra Info: ピークスコアモデル = "test1": [ { スコア名 = "強度", - 加重 = "-0.078328345434545", - 貢献度 = "-0.021" + 加重 = "-0.10947638732718", + 貢献度 = "-0.03" }, { スコア名 = "保持時間の差異", - 加重 = "-0.74923684676032", - 貢献度 = "0.066" + 加重 = "-0.768944834471997", + 貢献度 = "0.067" }, { スコア名 = "ライブラリ強度内積", - 加重 = "2.24238344148558", - 貢献度 = "0.081" + 加重 = "1.91473647678043", + 貢献度 = "0.071" }, { スコア名 = "形（加重）", - 加重 = "1.20618462186508", - 貢献度 = "0.081" + 加重 = "0.964673347739591", + 貢献度 = "0.064" }, { スコア名 = "共溶出（加重）", - 加重 = "0.0330641179011537", - 貢献度 = "-0.031" + 加重 = "0.0265095737294209", + 貢献度 = "-0.023" }, { スコア名 = "共溶出数", - 加重 = "0.151546153152723", - 貢献度 = "0.05" + 加重 = "0.182160151225063", + 貢献度 = "0.062" }, { スコア名 = "信号対ノイズ比", - 加重 = "0.176740916361492", - 貢献度 = "0.042" + 加重 = "0.222902489204878", + 貢献度 = "0.053" }, { スコア名 = "参照強度内積", - 加重 = "0.498299821042048", - 貢献度 = "0.02" + 加重 = "0.552867011319634", + 貢献度 = "0.023" }, { スコア名 = "参照形（加重）", - 加重 = "6.39974546904101", - 貢献度 = "0.4" + 加重 = "6.54328045047817", + 貢献度 = "0.406" }, { スコア名 = "参照共溶出（加重）", - 加重 = "-0.0482245507469112", - 貢献度 = "0.04" + 加重 = "-0.035670415865123", + 貢献度 = "0.028" }, { スコア名 = "参照共溶出数", - 加重 = "0.547648429894388", - 貢献度 = "0.1" + 加重 = "0.528458461601712", + 貢献度 = "0.099" }, { スコア名 = "標準強度", - 加重 = "0.628130085182893", - 貢献度 = "0.172" + 加重 = "0.658504481008043", + 貢献度 = "0.181" } ], デコイを使用する = 真, @@ -158,18 +158,18 @@ Summary : 「test1」を使用してピークが再積分されました All Info : 「test1」を使用してピークが再積分されました 再積分>ピークスコアモデルは"test1"です -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "強度", 加重 = "-0.078328345434545", 貢献度 = "-0.021" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "保持時間の差異", 加重 = "-0.74923684676032", 貢献度 = "0.066" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "ライブラリ強度内積", 加重 = "2.24238344148558", 貢献度 = "0.081" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "形（加重）", 加重 = "1.20618462186508", 貢献度 = "0.081" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出（加重）", 加重 = "0.0330641179011537", 貢献度 = "-0.031" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出数", 加重 = "0.151546153152723", 貢献度 = "0.05" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "信号対ノイズ比", 加重 = "0.176740916361492", 貢献度 = "0.042" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照強度内積", 加重 = "0.498299821042048", 貢献度 = "0.02" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照形（加重）", 加重 = "6.39974546904101", 貢献度 = "0.4" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出（加重）", 加重 = "-0.0482245507469112", 貢献度 = "0.04" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出数", 加重 = "0.547648429894388", 貢献度 = "0.1" }が含まれています -再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "標準強度", 加重 = "0.628130085182893", 貢献度 = "0.172" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "強度", 加重 = "-0.10947638732718", 貢献度 = "-0.03" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "保持時間の差異", 加重 = "-0.768944834471997", 貢献度 = "0.067" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "ライブラリ強度内積", 加重 = "1.91473647678043", 貢献度 = "0.071" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "形（加重）", 加重 = "0.964673347739591", 貢献度 = "0.064" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出（加重）", 加重 = "0.0265095737294209", 貢献度 = "-0.023" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "共溶出数", 加重 = "0.182160151225063", 貢献度 = "0.062" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "信号対ノイズ比", 加重 = "0.222902489204878", 貢献度 = "0.053" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照強度内積", 加重 = "0.552867011319634", 貢献度 = "0.023" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照形（加重）", 加重 = "6.54328045047817", 貢献度 = "0.406" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出（加重）", 加重 = "-0.035670415865123", 貢献度 = "0.028" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "参照共溶出数", 加重 = "0.528458461601712", 貢献度 = "0.099" }が含まれています +再積分>ピークスコアモデル>フィーチャースコア：{ スコア名 = "標準強度", 加重 = "0.658504481008043", 貢献度 = "0.181" }が含まれています 再積分>ピークスコアモデル>デコイを使用するは真です 再積分>ピークスコアモデル>2番目に良いピークを使用は偽です 再積分>有意なQ値のみを積分は真です @@ -181,63 +181,63 @@ Extra Info: ピークスコアモデル = "test1": [ { スコア名 = "強度", - 加重 = "-0.078328345434545", - 貢献度 = "-0.021" + 加重 = "-0.10947638732718", + 貢献度 = "-0.03" }, { スコア名 = "保持時間の差異", - 加重 = "-0.74923684676032", - 貢献度 = "0.066" + 加重 = "-0.768944834471997", + 貢献度 = "0.067" }, { スコア名 = "ライブラリ強度内積", - 加重 = "2.24238344148558", - 貢献度 = "0.081" + 加重 = "1.91473647678043", + 貢献度 = "0.071" }, { スコア名 = "形（加重）", - 加重 = "1.20618462186508", - 貢献度 = "0.081" + 加重 = "0.964673347739591", + 貢献度 = "0.064" }, { スコア名 = "共溶出（加重）", - 加重 = "0.0330641179011537", - 貢献度 = "-0.031" + 加重 = "0.0265095737294209", + 貢献度 = "-0.023" }, { スコア名 = "共溶出数", - 加重 = "0.151546153152723", - 貢献度 = "0.05" + 加重 = "0.182160151225063", + 貢献度 = "0.062" }, { スコア名 = "信号対ノイズ比", - 加重 = "0.176740916361492", - 貢献度 = "0.042" + 加重 = "0.222902489204878", + 貢献度 = "0.053" }, { スコア名 = "参照強度内積", - 加重 = "0.498299821042048", - 貢献度 = "0.02" + 加重 = "0.552867011319634", + 貢献度 = "0.023" }, { スコア名 = "参照形（加重）", - 加重 = "6.39974546904101", - 貢献度 = "0.4" + 加重 = "6.54328045047817", + 貢献度 = "0.406" }, { スコア名 = "参照共溶出（加重）", - 加重 = "-0.0482245507469112", - 貢献度 = "0.04" + 加重 = "-0.035670415865123", + 貢献度 = "0.028" }, { スコア名 = "参照共溶出数", - 加重 = "0.547648429894388", - 貢献度 = "0.1" + 加重 = "0.528458461601712", + 貢献度 = "0.099" }, { スコア名 = "標準強度", - 加重 = "0.628130085182893", - 貢献度 = "0.172" + 加重 = "0.658504481008043", + 貢献度 = "0.181" } ], デコイを使用する = 真, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestSrmTutorialLegacy.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestSrmTutorialLegacy.log index b7d3bbea13..b7caba5f7d 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestSrmTutorialLegacy.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestSrmTutorialLegacy.log @@ -307,8 +307,8 @@ Summary : 設定>トランジションの設定が変更されました All Info : トランジションの設定が変更されました 設定>トランジションの設定－予測>衝突エネルギーは"SCIEX"から"SRMcourse_20140211_Parameters_custom-CE-equation"に変更されました -設定>トランジションの設定－予測>衝突エネルギー>回帰パラメータ：{ 電荷 = "2", 傾き = "0.0369", 切片 = "3.9361" }が含まれています -設定>トランジションの設定－予測>衝突エネルギー>回帰パラメータ：{ 電荷 = "3", 傾き = "0.0208", 切片 = "9.0837" }が含まれています +設定>トランジションの設定－予測>衝突エネルギー>回帰パラメータ：{ 電荷 = "2", 傾き = "0.025", 切片 = "8.6852" }が含まれています +設定>トランジションの設定－予測>衝突エネルギー>回帰パラメータ：{ 電荷 = "3", 傾き = "0.046", 切片 = "-1.9754" }が含まれています 設定>トランジションの設定－装置>メソッド許容誤差m/zは"0.055"から"0.01"に変更されました Undo Redo : 結果が管理されました diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestPeakPickingTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestPeakPickingTutorial.log index 03bb4ca819..8f7bd0550f 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestPeakPickingTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestPeakPickingTutorial.log @@ -66,18 +66,18 @@ Summary : Reintegrated peaks using "test1" All Info : Reintegrated peaks using "test1" Reintegrate > Peak scoring model is "test1" -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,078328345434545", Percentage Contribution = "-0,021" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,74923684676032", Percentage Contribution = "0,066" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "2,24238344148558", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "1,20618462186508", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0330641179011537", Percentage Contribution = "-0,031" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,151546153152723", Percentage Contribution = "0,05" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,176740916361492", Percentage Contribution = "0,042" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,498299821042048", Percentage Contribution = "0,02" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,39974546904101", Percentage Contribution = "0,4" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,0482245507469112", Percentage Contribution = "0,04" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,547648429894388", Percentage Contribution = "0,1" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,628130085182893", Percentage Contribution = "0,172" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,10947638732718", Percentage Contribution = "-0,03" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,768944834471997", Percentage Contribution = "0,067" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "1,91473647678043", Percentage Contribution = "0,071" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "0,964673347739591", Percentage Contribution = "0,064" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0265095737294209", Percentage Contribution = "-0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,182160151225063", Percentage Contribution = "0,062" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,222902489204878", Percentage Contribution = "0,053" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,552867011319634", Percentage Contribution = "0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,54328045047817", Percentage Contribution = "0,406" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,035670415865123", Percentage Contribution = "0,028" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,528458461601712", Percentage Contribution = "0,099" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,658504481008043", Percentage Contribution = "0,181" } Reintegrate > Peak scoring model > Use decoys is True Reintegrate > Peak scoring model > Uses second best peaks is False Reintegrate > Integrate all peaks is True @@ -88,63 +88,63 @@ Extra Info: Peak scoring model = "test1": [ { Score Name = "Intensity", - Weight = "-0,078328345434545", - Percentage Contribution = "-0,021" + Weight = "-0,10947638732718", + Percentage Contribution = "-0,03" }, { Score Name = "Retention time difference", - Weight = "-0,74923684676032", - Percentage Contribution = "0,066" + Weight = "-0,768944834471997", + Percentage Contribution = "0,067" }, { Score Name = "Library intensity dot-product", - Weight = "2,24238344148558", - Percentage Contribution = "0,081" + Weight = "1,91473647678043", + Percentage Contribution = "0,071" }, { Score Name = "Shape (weighted)", - Weight = "1,20618462186508", - Percentage Contribution = "0,081" + Weight = "0,964673347739591", + Percentage Contribution = "0,064" }, { Score Name = "Co-elution (weighted)", - Weight = "0,0330641179011537", - Percentage Contribution = "-0,031" + Weight = "0,0265095737294209", + Percentage Contribution = "-0,023" }, { Score Name = "Co-elution count", - Weight = "0,151546153152723", - Percentage Contribution = "0,05" + Weight = "0,182160151225063", + Percentage Contribution = "0,062" }, { Score Name = "Signal to noise", - Weight = "0,176740916361492", - Percentage Contribution = "0,042" + Weight = "0,222902489204878", + Percentage Contribution = "0,053" }, { Score Name = "Reference intensity dot-product", - Weight = "0,498299821042048", - Percentage Contribution = "0,02" + Weight = "0,552867011319634", + Percentage Contribution = "0,023" }, { Score Name = "Reference shape (weighted)", - Weight = "6,39974546904101", - Percentage Contribution = "0,4" + Weight = "6,54328045047817", + Percentage Contribution = "0,406" }, { Score Name = "Reference co-elution (weighted)", - Weight = "-0,0482245507469112", - Percentage Contribution = "0,04" + Weight = "-0,035670415865123", + Percentage Contribution = "0,028" }, { Score Name = "Reference co-elution count", - Weight = "0,547648429894388", - Percentage Contribution = "0,1" + Weight = "0,528458461601712", + Percentage Contribution = "0,099" }, { Score Name = "Standard Intensity", - Weight = "0,628130085182893", - Percentage Contribution = "0,172" + Weight = "0,658504481008043", + Percentage Contribution = "0,181" } ], Use decoys = True, @@ -158,18 +158,18 @@ Summary : Reintegrated peaks using "test1" All Info : Reintegrated peaks using "test1" Reintegrate > Peak scoring model is "test1" -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,078328345434545", Percentage Contribution = "-0,021" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,74923684676032", Percentage Contribution = "0,066" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "2,24238344148558", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "1,20618462186508", Percentage Contribution = "0,081" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0330641179011537", Percentage Contribution = "-0,031" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,151546153152723", Percentage Contribution = "0,05" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,176740916361492", Percentage Contribution = "0,042" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,498299821042048", Percentage Contribution = "0,02" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,39974546904101", Percentage Contribution = "0,4" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,0482245507469112", Percentage Contribution = "0,04" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,547648429894388", Percentage Contribution = "0,1" } -Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,628130085182893", Percentage Contribution = "0,172" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Intensity", Weight = "-0,10947638732718", Percentage Contribution = "-0,03" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Retention time difference", Weight = "-0,768944834471997", Percentage Contribution = "0,067" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Library intensity dot-product", Weight = "1,91473647678043", Percentage Contribution = "0,071" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Shape (weighted)", Weight = "0,964673347739591", Percentage Contribution = "0,064" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution (weighted)", Weight = "0,0265095737294209", Percentage Contribution = "-0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Co-elution count", Weight = "0,182160151225063", Percentage Contribution = "0,062" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Signal to noise", Weight = "0,222902489204878", Percentage Contribution = "0,053" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference intensity dot-product", Weight = "0,552867011319634", Percentage Contribution = "0,023" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference shape (weighted)", Weight = "6,54328045047817", Percentage Contribution = "0,406" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution (weighted)", Weight = "-0,035670415865123", Percentage Contribution = "0,028" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Reference co-elution count", Weight = "0,528458461601712", Percentage Contribution = "0,099" } +Reintegrate > Peak scoring model > Feature scores : contains { Score Name = "Standard Intensity", Weight = "0,658504481008043", Percentage Contribution = "0,181" } Reintegrate > Peak scoring model > Use decoys is True Reintegrate > Peak scoring model > Uses second best peaks is False Reintegrate > Only integrate significant q values is True @@ -181,63 +181,63 @@ Extra Info: Peak scoring model = "test1": [ { Score Name = "Intensity", - Weight = "-0,078328345434545", - Percentage Contribution = "-0,021" + Weight = "-0,10947638732718", + Percentage Contribution = "-0,03" }, { Score Name = "Retention time difference", - Weight = "-0,74923684676032", - Percentage Contribution = "0,066" + Weight = "-0,768944834471997", + Percentage Contribution = "0,067" }, { Score Name = "Library intensity dot-product", - Weight = "2,24238344148558", - Percentage Contribution = "0,081" + Weight = "1,91473647678043", + Percentage Contribution = "0,071" }, { Score Name = "Shape (weighted)", - Weight = "1,20618462186508", - Percentage Contribution = "0,081" + Weight = "0,964673347739591", + Percentage Contribution = "0,064" }, { Score Name = "Co-elution (weighted)", - Weight = "0,0330641179011537", - Percentage Contribution = "-0,031" + Weight = "0,0265095737294209", + Percentage Contribution = "-0,023" }, { Score Name = "Co-elution count", - Weight = "0,151546153152723", - Percentage Contribution = "0,05" + Weight = "0,182160151225063", + Percentage Contribution = "0,062" }, { Score Name = "Signal to noise", - Weight = "0,176740916361492", - Percentage Contribution = "0,042" + Weight = "0,222902489204878", + Percentage Contribution = "0,053" }, { Score Name = "Reference intensity dot-product", - Weight = "0,498299821042048", - Percentage Contribution = "0,02" + Weight = "0,552867011319634", + Percentage Contribution = "0,023" }, { Score Name = "Reference shape (weighted)", - Weight = "6,39974546904101", - Percentage Contribution = "0,4" + Weight = "6,54328045047817", + Percentage Contribution = "0,406" }, { Score Name = "Reference co-elution (weighted)", - Weight = "-0,0482245507469112", - Percentage Contribution = "0,04" + Weight = "-0,035670415865123", + Percentage Contribution = "0,028" }, { Score Name = "Reference co-elution count", - Weight = "0,547648429894388", - Percentage Contribution = "0,1" + Weight = "0,528458461601712", + Percentage Contribution = "0,099" }, { Score Name = "Standard Intensity", - Weight = "0,628130085182893", - Percentage Contribution = "0,172" + Weight = "0,658504481008043", + Percentage Contribution = "0,181" } ], Use decoys = True, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestSrmTutorialLegacy.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestSrmTutorialLegacy.log index c74dfe788b..cbb9ed8797 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestSrmTutorialLegacy.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestSrmTutorialLegacy.log @@ -307,8 +307,8 @@ Summary : Settings > Transition Settings changed All Info : Transition Settings changed Settings > Transition Settings -- Prediction > Collision energy changed from "SCIEX" to "SRMcourse_20140211_Parameters_custom-CE-equation" -Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "2", Slope = "0,0369", Intercept = "3,9361" } -Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "3", Slope = "0,0208", Intercept = "9,0837" } +Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "2", Slope = "0,025", Intercept = "8,6852" } +Settings > Transition Settings -- Prediction > Collision energy > Regression parameters : contains { Charge = "3", Slope = "0,046", Intercept = "-1,9754" } Settings > Transition Settings -- Instrument > Method match tolerance m/z changed from "0,055" to "0,01" Undo Redo : Managed results diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestPeakPickingTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestPeakPickingTutorial.log index d1967ceef5..2c24d60fbd 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestPeakPickingTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestPeakPickingTutorial.log @@ -66,18 +66,18 @@ Summary : 已使用“test1”重新合并峰 All Info : 已使用“test1”重新合并峰 重新合并 > 峰得分模型 是 "test1" -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "强度", 权重 = "-0.078328345434545", 贡献百分比 = "-0.021" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "保留时间差异", 权重 = "-0.74923684676032", 贡献百分比 = "0.066" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "库强度点积", 权重 = "2.24238344148558", 贡献百分比 = "0.081" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "形状（权重）", 权重 = "1.20618462186508", 贡献百分比 = "0.081" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱（权重）", 权重 = "0.0330641179011537", 贡献百分比 = "-0.031" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱计数", 权重 = "0.151546153152723", 贡献百分比 = "0.05" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "噪声信号", 权重 = "0.176740916361492", 贡献百分比 = "0.042" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考强度点积", 权重 = "0.498299821042048", 贡献百分比 = "0.02" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考形状（权重）", 权重 = "6.39974546904101", 贡献百分比 = "0.4" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱（权重）", 权重 = "-0.0482245507469112", 贡献百分比 = "0.04" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱计数", 权重 = "0.547648429894388", 贡献百分比 = "0.1" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "标准强度", 权重 = "0.628130085182893", 贡献百分比 = "0.172" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "强度", 权重 = "-0.10947638732718", 贡献百分比 = "-0.03" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "保留时间差异", 权重 = "-0.768944834471997", 贡献百分比 = "0.067" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "库强度点积", 权重 = "1.91473647678043", 贡献百分比 = "0.071" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "形状（权重）", 权重 = "0.964673347739591", 贡献百分比 = "0.064" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱（权重）", 权重 = "0.0265095737294209", 贡献百分比 = "-0.023" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱计数", 权重 = "0.182160151225063", 贡献百分比 = "0.062" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "噪声信号", 权重 = "0.222902489204878", 贡献百分比 = "0.053" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考强度点积", 权重 = "0.552867011319634", 贡献百分比 = "0.023" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考形状（权重）", 权重 = "6.54328045047817", 贡献百分比 = "0.406" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱（权重）", 权重 = "-0.035670415865123", 贡献百分比 = "0.028" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱计数", 权重 = "0.528458461601712", 贡献百分比 = "0.099" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "标准强度", 权重 = "0.658504481008043", 贡献百分比 = "0.181" } 重新合并 > 峰得分模型 > 采用诱饵 是 真 重新合并 > 峰得分模型 > 采用次优峰值 是 假 重新合并 > 积分所有峰 是 真 @@ -88,63 +88,63 @@ Extra Info: 峰得分模型 = "test1": [ { 得分名称 = "强度", - 权重 = "-0.078328345434545", - 贡献百分比 = "-0.021" + 权重 = "-0.10947638732718", + 贡献百分比 = "-0.03" }, { 得分名称 = "保留时间差异", - 权重 = "-0.74923684676032", - 贡献百分比 = "0.066" + 权重 = "-0.768944834471997", + 贡献百分比 = "0.067" }, { 得分名称 = "库强度点积", - 权重 = "2.24238344148558", - 贡献百分比 = "0.081" + 权重 = "1.91473647678043", + 贡献百分比 = "0.071" }, { 得分名称 = "形状（权重）", - 权重 = "1.20618462186508", - 贡献百分比 = "0.081" + 权重 = "0.964673347739591", + 贡献百分比 = "0.064" }, { 得分名称 = "共洗脱（权重）", - 权重 = "0.0330641179011537", - 贡献百分比 = "-0.031" + 权重 = "0.0265095737294209", + 贡献百分比 = "-0.023" }, { 得分名称 = "共洗脱计数", - 权重 = "0.151546153152723", - 贡献百分比 = "0.05" + 权重 = "0.182160151225063", + 贡献百分比 = "0.062" }, { 得分名称 = "噪声信号", - 权重 = "0.176740916361492", - 贡献百分比 = "0.042" + 权重 = "0.222902489204878", + 贡献百分比 = "0.053" }, { 得分名称 = "参考强度点积", - 权重 = "0.498299821042048", - 贡献百分比 = "0.02" + 权重 = "0.552867011319634", + 贡献百分比 = "0.023" }, { 得分名称 = "参考形状（权重）", - 权重 = "6.39974546904101", - 贡献百分比 = "0.4" + 权重 = "6.54328045047817", + 贡献百分比 = "0.406" }, { 得分名称 = "参考共洗脱（权重）", - 权重 = "-0.0482245507469112", - 贡献百分比 = "0.04" + 权重 = "-0.035670415865123", + 贡献百分比 = "0.028" }, { 得分名称 = "参考共洗脱计数", - 权重 = "0.547648429894388", - 贡献百分比 = "0.1" + 权重 = "0.528458461601712", + 贡献百分比 = "0.099" }, { 得分名称 = "标准强度", - 权重 = "0.628130085182893", - 贡献百分比 = "0.172" + 权重 = "0.658504481008043", + 贡献百分比 = "0.181" } ], 采用诱饵 = 真, @@ -158,18 +158,18 @@ Summary : 已使用“test1”重新合并峰 All Info : 已使用“test1”重新合并峰 重新合并 > 峰得分模型 是 "test1" -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "强度", 权重 = "-0.078328345434545", 贡献百分比 = "-0.021" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "保留时间差异", 权重 = "-0.74923684676032", 贡献百分比 = "0.066" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "库强度点积", 权重 = "2.24238344148558", 贡献百分比 = "0.081" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "形状（权重）", 权重 = "1.20618462186508", 贡献百分比 = "0.081" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱（权重）", 权重 = "0.0330641179011537", 贡献百分比 = "-0.031" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱计数", 权重 = "0.151546153152723", 贡献百分比 = "0.05" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "噪声信号", 权重 = "0.176740916361492", 贡献百分比 = "0.042" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考强度点积", 权重 = "0.498299821042048", 贡献百分比 = "0.02" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考形状（权重）", 权重 = "6.39974546904101", 贡献百分比 = "0.4" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱（权重）", 权重 = "-0.0482245507469112", 贡献百分比 = "0.04" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱计数", 权重 = "0.547648429894388", 贡献百分比 = "0.1" } -重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "标准强度", 权重 = "0.628130085182893", 贡献百分比 = "0.172" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "强度", 权重 = "-0.10947638732718", 贡献百分比 = "-0.03" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "保留时间差异", 权重 = "-0.768944834471997", 贡献百分比 = "0.067" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "库强度点积", 权重 = "1.91473647678043", 贡献百分比 = "0.071" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "形状（权重）", 权重 = "0.964673347739591", 贡献百分比 = "0.064" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱（权重）", 权重 = "0.0265095737294209", 贡献百分比 = "-0.023" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "共洗脱计数", 权重 = "0.182160151225063", 贡献百分比 = "0.062" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "噪声信号", 权重 = "0.222902489204878", 贡献百分比 = "0.053" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考强度点积", 权重 = "0.552867011319634", 贡献百分比 = "0.023" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考形状（权重）", 权重 = "6.54328045047817", 贡献百分比 = "0.406" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱（权重）", 权重 = "-0.035670415865123", 贡献百分比 = "0.028" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "参考共洗脱计数", 权重 = "0.528458461601712", 贡献百分比 = "0.099" } +重新合并 > 峰得分模型 > 特征得分 : 包含 { 得分名称 = "标准强度", 权重 = "0.658504481008043", 贡献百分比 = "0.181" } 重新合并 > 峰得分模型 > 采用诱饵 是 真 重新合并 > 峰得分模型 > 采用次优峰值 是 假 重新合并 > 仅积分有显著性 q 值的峰 是 真 @@ -181,63 +181,63 @@ Extra Info: 峰得分模型 = "test1": [ { 得分名称 = "强度", - 权重 = "-0.078328345434545", - 贡献百分比 = "-0.021" + 权重 = "-0.10947638732718", + 贡献百分比 = "-0.03" }, { 得分名称 = "保留时间差异", - 权重 = "-0.74923684676032", - 贡献百分比 = "0.066" + 权重 = "-0.768944834471997", + 贡献百分比 = "0.067" }, { 得分名称 = "库强度点积", - 权重 = "2.24238344148558", - 贡献百分比 = "0.081" + 权重 = "1.91473647678043", + 贡献百分比 = "0.071" }, { 得分名称 = "形状（权重）", - 权重 = "1.20618462186508", - 贡献百分比 = "0.081" + 权重 = "0.964673347739591", + 贡献百分比 = "0.064" }, { 得分名称 = "共洗脱（权重）", - 权重 = "0.0330641179011537", - 贡献百分比 = "-0.031" + 权重 = "0.0265095737294209", + 贡献百分比 = "-0.023" }, { 得分名称 = "共洗脱计数", - 权重 = "0.151546153152723", - 贡献百分比 = "0.05" + 权重 = "0.182160151225063", + 贡献百分比 = "0.062" }, { 得分名称 = "噪声信号", - 权重 = "0.176740916361492", - 贡献百分比 = "0.042" + 权重 = "0.222902489204878", + 贡献百分比 = "0.053" }, { 得分名称 = "参考强度点积", - 权重 = "0.498299821042048", - 贡献百分比 = "0.02" + 权重 = "0.552867011319634", + 贡献百分比 = "0.023" }, { 得分名称 = "参考形状（权重）", - 权重 = "6.39974546904101", - 贡献百分比 = "0.4" + 权重 = "6.54328045047817", + 贡献百分比 = "0.406" }, { 得分名称 = "参考共洗脱（权重）", - 权重 = "-0.0482245507469112", - 贡献百分比 = "0.04" + 权重 = "-0.035670415865123", + 贡献百分比 = "0.028" }, { 得分名称 = "参考共洗脱计数", - 权重 = "0.547648429894388", - 贡献百分比 = "0.1" + 权重 = "0.528458461601712", + 贡献百分比 = "0.099" }, { 得分名称 = "标准强度", - 权重 = "0.628130085182893", - 贡献百分比 = "0.172" + 权重 = "0.658504481008043", + 贡献百分比 = "0.181" } ], 采用诱饵 = 真, diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestSrmTutorialLegacy.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestSrmTutorialLegacy.log index c286f1a614..d23b2c90c5 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestSrmTutorialLegacy.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestSrmTutorialLegacy.log @@ -307,8 +307,8 @@ Summary : 设置 > 离子对设置 已更改 All Info : 离子对设置 已更改 设置 > 离子对设置 -- 预测 > 碰撞能量 从 "SCIEX" 更改到 "SRMcourse_20140211_Parameters_custom-CE-equation" -设置 > 离子对设置 -- 预测 > 碰撞能量 > 回归参数 : 包含 { 电荷 = "2", 斜率 = "0.0369", 截距 = "3.9361" } -设置 > 离子对设置 -- 预测 > 碰撞能量 > 回归参数 : 包含 { 电荷 = "3", 斜率 = "0.0208", 截距 = "9.0837" } +设置 > 离子对设置 -- 预测 > 碰撞能量 > 回归参数 : 包含 { 电荷 = "2", 斜率 = "0.025", 截距 = "8.6852" } +设置 > 离子对设置 -- 预测 > 碰撞能量 > 回归参数 : 包含 { 电荷 = "3", 斜率 = "0.046", 截距 = "-1.9754" } 设置 > 离子对设置 -- 仪器 > 方法匹配耐受性质荷比 从 "0.055" 更改到 "0.01" Undo Redo : 已管理结果 From ee6e2c7994f411b5f1ce199c4a1ffad94a836b6b Mon Sep 17 00:00:00 2001 From: Nicholas Shulman Date: Tue, 14 Nov 2023 17:13:50 -0800 Subject: [PATCH 13/14] Change expected number of transitions in TestAsymCEOpt --- pwiz_tools/Skyline/TestData/Results/AsymCEOptTest.cs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pwiz_tools/Skyline/TestData/Results/AsymCEOptTest.cs b/pwiz_tools/Skyline/TestData/Results/AsymCEOptTest.cs index 2769851db0..120521a704 100644 --- a/pwiz_tools/Skyline/TestData/Results/AsymCEOptTest.cs +++ b/pwiz_tools/Skyline/TestData/Results/AsymCEOptTest.cs @@ -64,7 +64,7 @@ private void ExportImport(ResultsTestDocumentContainer docContainer, string resu var chromSet = new ChromatogramSet("Optimize", new[] {resultsUri}, Annotations.EMPTY, optRegression); var measuredResults = new MeasuredResults(new[] { chromSet }); - docContainer.ChangeMeasuredResults(measuredResults, 2, optSteps1 + optSteps2, 5*optSteps1 + 5*optSteps2); + docContainer.ChangeMeasuredResults(measuredResults, 2, optSteps1 + optSteps2, 86); // Check expected optimization data with missing values for steps below 10 volts CE int expectedMissingSteps = optSteps - optSteps1; From 8e1da0f2f53f5a6199fbfc7dcee7c3d50bf22dd3 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Mon, 20 Nov 2023 12:07:54 -0500 Subject: [PATCH 14/14] * removed ignoreScheduledLimitsForChromatograms (it will always be enabled for Sciex) --- pwiz/data/msdata/Reader.cpp | 2 -- pwiz/data/msdata/Reader.hpp | 4 ---- pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp | 6 ++++-- pwiz/utility/bindings/CLI/msdata/Reader.cpp | 1 - pwiz/utility/bindings/CLI/msdata/Reader.hpp | 7 ------- pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs | 3 +-- pwiz_tools/commandline/msconvert.cpp | 3 --- 7 files changed, 5 insertions(+), 21 deletions(-) diff --git a/pwiz/data/msdata/Reader.cpp b/pwiz/data/msdata/Reader.cpp index 8ab14325e8..577f073770 100755 --- a/pwiz/data/msdata/Reader.cpp +++ b/pwiz/data/msdata/Reader.cpp @@ -52,7 +52,6 @@ Reader::Config::Config() , sortAndJitter(false) , globalChromatogramsAreMs1Only(false) , ddaProcessing(false) - , ignoreScheduledLimitsForChromatograms(false) { } @@ -75,7 +74,6 @@ Reader::Config::Config(const Config& rhs) isolationMzAndMobilityFilter = rhs.isolationMzAndMobilityFilter; sortAndJitter = rhs.sortAndJitter; globalChromatogramsAreMs1Only = rhs.globalChromatogramsAreMs1Only; - ignoreScheduledLimitsForChromatograms = rhs.ignoreScheduledLimitsForChromatograms; } // default implementation; most Readers don't need to worry about multi-run input files diff --git a/pwiz/data/msdata/Reader.hpp b/pwiz/data/msdata/Reader.hpp index 8d7edd38b5..c119a305b7 100755 --- a/pwiz/data/msdata/Reader.hpp +++ b/pwiz/data/msdata/Reader.hpp @@ -96,10 +96,6 @@ class PWIZ_API_DECL Reader // to the same precursor from the same survey scan, and lockmass-correcting the precursor mass (if the lockmass refiner is active). bool ddaProcessing; - /// when true, scheduled SIM/SRM chromatograms will try to get an XIC covering the entire range instead of just the scheduled range - /// (useful if the instrument recorded extra data outside the scheduled limits, currently only applicable to Sciex WIFF) - bool ignoreScheduledLimitsForChromatograms; - Config(); Config(const Config& rhs); }; diff --git a/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp b/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp index 1a18eb605b..6d7652ee12 100644 --- a/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp +++ b/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp @@ -251,7 +251,8 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D result->setTimeIntensityArrays(std::vector(), std::vector(), UO_minute, MS_number_of_detector_counts); pwiz::util::BinaryData times, intensities; - experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms); + bool ignoreScheduledLimitsForChromatograms = true; + experiment->getSIC(ie.transition, times, intensities, ignoreScheduledLimitsForChromatograms); result->defaultArrayLength = times.size(); if (getBinaryData) @@ -290,7 +291,8 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D result->setTimeIntensityArrays(std::vector(), std::vector(), UO_minute, MS_number_of_detector_counts); pwiz::util::BinaryData times, intensities; - experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms); + bool ignoreScheduledLimitsForChromatograms = true; + experiment->getSIC(ie.transition, times, intensities, ignoreScheduledLimitsForChromatograms); result->defaultArrayLength = times.size(); if (getBinaryData) diff --git a/pwiz/utility/bindings/CLI/msdata/Reader.cpp b/pwiz/utility/bindings/CLI/msdata/Reader.cpp index eab2e27632..4cb643fcd3 100644 --- a/pwiz/utility/bindings/CLI/msdata/Reader.cpp +++ b/pwiz/utility/bindings/CLI/msdata/Reader.cpp @@ -86,7 +86,6 @@ static void copyReaderConfig(pwiz::msdata::Reader::Config& config, ReaderConfig^ config.sortAndJitter = readerConfig->sortAndJitter; config.globalChromatogramsAreMs1Only = readerConfig->globalChromatogramsAreMs1Only; config.ddaProcessing = readerConfig->ddaProcessing; - config.ignoreScheduledLimitsForChromatograms = readerConfig->ignoreScheduledLimitsForChromatograms; if (readerConfig->isolationMzAndMobilityFilter != nullptr) for each (MzMobilityWindow^ filter in readerConfig->isolationMzAndMobilityFilter) diff --git a/pwiz/utility/bindings/CLI/msdata/Reader.hpp b/pwiz/utility/bindings/CLI/msdata/Reader.hpp index de8157474a..11f7dafeb9 100644 --- a/pwiz/utility/bindings/CLI/msdata/Reader.hpp +++ b/pwiz/utility/bindings/CLI/msdata/Reader.hpp @@ -145,12 +145,6 @@ public ref class ReaderConfig /// bool ddaProcessing; - /// - /// when true, scheduled SIM/SRM chromatograms will try to get an XIC covering the entire range instead of just the scheduled range - /// (useful if the instrument recorded extra data outside the scheduled limits, currently only applicable to Sciex WIFF) - /// - bool ignoreScheduledLimitsForChromatograms; - ReaderConfig() : simAsSpectra(false) , srmAsSpectra(false) @@ -166,7 +160,6 @@ public ref class ReaderConfig , sortAndJitter(false) , globalChromatogramsAreMs1Only(false) , ddaProcessing(false) - , ignoreScheduledLimitsForChromatograms(false) { } }; diff --git a/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs b/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs index a5a26f1acb..f61aa7d74e 100644 --- a/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs +++ b/pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs @@ -193,8 +193,7 @@ public MsDataFileImpl(string path, int sampleIndex = 0, LockMassParameters lockm combineIonMobilitySpectra = !ForceUncombinedIonMobility && combineIonMobilitySpectra, ignoreCalibrationScans = true, // For Waters, we don't need to hear about lockmass values reportSonarBins = true, // For Waters SONAR data, report bin number instead of false drift time - globalChromatogramsAreMs1Only = true, - ignoreScheduledLimitsForChromatograms = true + globalChromatogramsAreMs1Only = true }; _lockmassParameters = lockmassParameters; FULL_READER_LIST.read(path, _msDataFile, sampleIndex, _config); diff --git a/pwiz_tools/commandline/msconvert.cpp b/pwiz_tools/commandline/msconvert.cpp index d56d3d5fad..eb4bda1112 100644 --- a/pwiz_tools/commandline/msconvert.cpp +++ b/pwiz_tools/commandline/msconvert.cpp @@ -448,9 +448,6 @@ Config parseCommandLine(int argc, char** argv) ("ignoreCalibrationScans", po::value(&config.ignoreCalibrationScans)->zero_tokens(), ": do not process calibration scans (currently only applies to Waters lockmass function)") - ("ignoreScheduledLimitsForChromatograms", - po::value(&config.ignoreScheduledLimitsForChromatograms)->zero_tokens(), - ": scheduled SIM/SRM chromatograms will try to get an XIC covering the entire run time instead of just the scheduled limits") ("acceptZeroLengthSpectra", po::value(&config.acceptZeroLengthSpectra)->zero_tokens(), ": some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file")