internal static MassSpecMethod ExtractMsMethod(IAcqMethod dataAcqMethod)
{
if (dataAcqMethod == null)
{
return(null);
}
const int kMsMethodDeviceType = 0; // device type for MassSpecMethod
int devType; // device type
EnumDeviceMethods enumMethod = (EnumDeviceMethods)dataAcqMethod;
enumMethod.Reset();
do
{
object devMethod; // one of the sub-methods
int devModel; // device model
int devInst; // device instrument type
enumMethod.Next(out devMethod, out devType, out devModel, out devInst);
if (devType == kMsMethodDeviceType)
{
return((MassSpecMethod)devMethod);
}
if (devType == -1)
{
//Call Err.Raise(1, "ExtractMSMethod", "No MS method found")
return(null);
}
}while (devType == kMsMethodDeviceType);
return(null);
}
internal static IAcqMethod GetAcqMethod(string methodFilePath, out MassSpecMethod templateMsMethod)
{
ApplicationClass analyst = new ApplicationClass();
// Make sure that Analyst is fully started
IAcqMethodDirConfig acqMethodDir = (IAcqMethodDirConfig)analyst.Acquire();
if (acqMethodDir == null)
{
throw new IOException("Failed to initialize. Analyst may need to be started.");
}
object acqMethodObj;
acqMethodDir.LoadNonUIMethod(methodFilePath, out acqMethodObj);
IAcqMethod templateAcqMethod = (IAcqMethod)acqMethodObj;
templateMsMethod = ExtractMsMethod(templateAcqMethod);
return(templateAcqMethod);
}
public override void build()
{
MassSpecMethod templateMsMethod;
IAcqMethod templateAcqMethod = GetAcqMethod(TemplateMethod, out templateMsMethod);
ValidateMethod(templateMsMethod);
foreach (var methodTranList in MethodTrans)
{
Console.Error.WriteLine(string.Format("MESSAGE: Exporting method {0}", Path.GetFileName(methodTranList.FinalMethod)));
if (string.IsNullOrEmpty(methodTranList.TransitionList))
{
throw new IOException(string.Format("Failure creating method file {0}. The transition list is empty.", methodTranList.FinalMethod));
}
try
{
WriteToTemplate(templateAcqMethod, methodTranList);
}
catch (Exception x)
{
throw new IOException(string.Format("Failure creating method file {0}. {1}", methodTranList.FinalMethod, x.Message));
}
if (!File.Exists(methodTranList.OutputMethod))
{
throw new IOException(string.Format("Failure creating method file {0}.", methodTranList.FinalMethod));
}
// Skyline uses a segmented progress status, which expects 100% for each
// segment, with one segment per file.
Console.Error.WriteLine("100%");
}
}
public void WriteToTemplate(String templateMethodFile, MethodTransitions transitions)
{
MassSpecMethod templateMsMethod;
IAcqMethod templateAcqMethod = GetAcqMethod(TemplateMethod, out templateMsMethod);
var method = ExtractMsMethod(templateAcqMethod);
if (InclusionList || ScheduledMethod)
{
WriteToIDATemplate(method, transitions);
}
else
{
WriteToTargetedMSMSTemplate(method, transitions);
}
templateAcqMethod.SaveAcqMethodToFile(transitions.OutputMethod, 1);
if (ExportMultiQuant)
{
ExportMultiQuantTextMethod(transitions);
}
}
private void WriteToTemplate(IAcqMethod acqMethod, MethodTransitions transitions)
{
var method = ExtractMsMethod(acqMethod);
// Get the last period in the given template method.
// We will add transitions to the last period only.
var period = (Period)method.GetPeriod(method.PeriodCount - 1);
var msExperiment = (Experiment)period.GetExperiment(0);
double?triggerThreshold = transitions.Transitions[0].Threshold;
bool analystSupportsEnhancedScheduledMrm = AnalystSupportsEnhancedScheduledMrm(msExperiment);
if (triggerThreshold.HasValue && analystSupportsEnhancedScheduledMrm)
{
IExperiment8 experimentEnhanced = (IExperiment8)msExperiment;
experimentEnhanced.IsEnhancedsMRM = 1;
}
if (!triggerThreshold.HasValue && msExperiment.MassRangesCount > 0 && analystSupportsEnhancedScheduledMrm && ((IMassRange4)msExperiment.GetMassRange(0)).TriggerThreshold > 0)
{
triggerThreshold = ((IMassRange4)msExperiment.GetMassRange(0)).TriggerThreshold;
}
var templateMassRangeParams = (ParamDataColl)((IMassRange)msExperiment.GetMassRange(0)).MassDepParamTbl;
short templateCxpParameterIdx;
var templateCxp = (ParameterData)templateMassRangeParams.FindParameter("CXP", out templateCxpParameterIdx);
short templateSvParameterIdx;
var templateSv = (ParameterData)templateMassRangeParams.FindParameter("SV", out templateSvParameterIdx);
msExperiment.DeleteAllMasses();
float?medianArea = null;
float?minArea = null;
int count = transitions.Transitions.Count();
if (count >= 2)
{
var orderedTransitions = transitions.Transitions.OrderBy(t => t.AveragePeakArea);
medianArea = orderedTransitions.ElementAt((int)(count * Properties.Settings.Default.FractionOfTranstionsToUseDwellWeighting)).AveragePeakArea
+ orderedTransitions.ElementAt((int)((count - 1) * Properties.Settings.Default.FractionOfTranstionsToUseDwellWeighting)).AveragePeakArea;
medianArea /= 2;
minArea = transitions.Transitions.Min(t => t.AveragePeakArea);
}
foreach (var transition in transitions.Transitions)
{
int i;
var msMassRange = (MassRange)msExperiment.CreateMassRange(out i);
var msMassRange3 = (IMassRange3)msMassRange;
msMassRange.SetMassRange(transition.PrecursorMz, 0, transition.ProductMz);
msMassRange.DwellTime = transition.Dwell;
msMassRange3.CompoundID = transition.Label;
var massRangeParams = (ParamDataColl)msMassRange.MassDepParamTbl;
short s;
massRangeParams.Description = transition.Label;
massRangeParams.AddSetParameter("DP", (float)transition.DP, (float)transition.DP, 0, out s);
massRangeParams.AddSetParameter("CE", (float)transition.CE, (float)transition.CE, 0, out s);
if (templateCxpParameterIdx > 0 && templateCxp != null)
{
massRangeParams.AddSetParameter("CXP", templateCxp.startVal, templateCxp.stopVal, templateCxp.stepVal, out s);
}
if (templateSvParameterIdx > 0 && templateSv != null)
{
massRangeParams.AddSetParameter("SV", templateSv.startVal, templateSv.stopVal, templateSv.stepVal, out s);
}
if (transition.CoV.HasValue)
{
massRangeParams.AddSetParameter("COV", (float)transition.CoV, (float)transition.CoV, 0, out s);
}
if (analystSupportsEnhancedScheduledMrm)
{
var msMassRange4 = (IMassRange4)msMassRange;
var groupId = transition.Group;
msMassRange4.GroupID = groupId;
msMassRange4.IsPrimary = transition.Primary.HasValue && transition.Primary.Value == 2 ? 0 : 1;
msMassRange4.TriggerThreshold = triggerThreshold.HasValue ? triggerThreshold.Value : Properties.Settings.Default.MinTriggerThreshold;
double?detectionWindow = transitions.Transitions.Where(t => t.Group == groupId).Max(t => t.VariableRtWindow);
msMassRange4.DetectionWindow = detectionWindow.HasValue ? detectionWindow.Value * 60 : msMassRange4.DetectionWindow;
if (medianArea.HasValue && minArea.HasValue && minArea != medianArea && transition.AveragePeakArea.HasValue && transition.AveragePeakArea < medianArea)
{
double averageArea = transition.AveragePeakArea >= 1 ? (double)transition.AveragePeakArea : 1.0;
double scaledArea = (Math.Log(averageArea - minArea.Value + 1) / Math.Log((double)medianArea))
* (Properties.Settings.Default.MaxDwellWeightingForTargets - Properties.Settings.Default.MinDwellWeightingForTargets);
msMassRange4.DwellWeighting = Properties.Settings.Default.MaxDwellWeightingForTargets - scaledArea;
}
else
{
msMassRange4.DwellWeighting = 1.0;
}
}
}
acqMethod.SaveAcqMethodToFile(transitions.OutputMethod, 1);
}
internal static MassSpecMethod ExtractMsMethod(IAcqMethod dataAcqMethod)
{
if (dataAcqMethod == null)
return null;
const int kMsMethodDeviceType = 0; // device type for MassSpecMethod
int devType; // device type
EnumDeviceMethods enumMethod = (EnumDeviceMethods)dataAcqMethod;
enumMethod.Reset();
do
{
object devMethod; // one of the sub-methods
int devModel; // device model
int devInst; // device instrument type
enumMethod.Next(out devMethod, out devType, out devModel, out devInst);
if (devType == kMsMethodDeviceType)
return (MassSpecMethod)devMethod;
if (devType == -1)
{
//Call Err.Raise(1, "ExtractMSMethod", "No MS method found")
return null;
}
}
while (devType == kMsMethodDeviceType);
return null;
}
private void WriteToTemplate(IAcqMethod acqMethod, MethodTransitions transitions)
{
var method = ExtractMsMethod(acqMethod);
// Get the last period in the given template method.
// We will add transitions to the last period only.
var period = (Period)method.GetPeriod(method.PeriodCount - 1);
var msExperiment = (Experiment)period.GetExperiment(0);
double? triggerThreshold = transitions.Transitions[0].Threshold;
bool analystSupportsEnhancedScheduledMrm = AnalystSupportsEnhancedScheduledMrm(msExperiment);
if (triggerThreshold.HasValue && analystSupportsEnhancedScheduledMrm)
{
IExperiment8 experimentEnhanced = (IExperiment8)msExperiment;
experimentEnhanced.IsEnhancedsMRM = 1;
}
if (!triggerThreshold.HasValue && msExperiment.MassRangesCount > 0 && analystSupportsEnhancedScheduledMrm && ((IMassRange4)msExperiment.GetMassRange(0)).TriggerThreshold > 0)
{
triggerThreshold = ((IMassRange4)msExperiment.GetMassRange(0)).TriggerThreshold;
}
var templateMassRangeParams = (ParamDataColl)((IMassRange)msExperiment.GetMassRange(0)).MassDepParamTbl;
short templateCxpParameterIdx;
var templateCxp = (ParameterData)templateMassRangeParams.FindParameter("CXP", out templateCxpParameterIdx);
short templateSvParameterIdx;
var templateSv = (ParameterData)templateMassRangeParams.FindParameter("SV", out templateSvParameterIdx);
msExperiment.DeleteAllMasses();
float? medianArea = null;
float? minArea = null;
int count = transitions.Transitions.Count();
if (count >= 2)
{
var orderedTransitions = transitions.Transitions.OrderBy(t => t.AveragePeakArea);
medianArea = orderedTransitions.ElementAt((int)(count * Properties.Settings.Default.FractionOfTranstionsToUseDwellWeighting)).AveragePeakArea
+ orderedTransitions.ElementAt((int)((count - 1) * Properties.Settings.Default.FractionOfTranstionsToUseDwellWeighting)).AveragePeakArea;
medianArea /= 2;
minArea = transitions.Transitions.Min(t => t.AveragePeakArea);
}
foreach (var transition in transitions.Transitions)
{
int i;
var msMassRange = (MassRange) msExperiment.CreateMassRange(out i);
var msMassRange3 = (IMassRange3) msMassRange;
msMassRange.SetMassRange(transition.PrecursorMz, 0, transition.ProductMz);
msMassRange.DwellTime = transition.Dwell;
msMassRange3.CompoundID = transition.Label;
var massRangeParams = (ParamDataColl) msMassRange.MassDepParamTbl;
short s;
massRangeParams.Description = transition.Label;
massRangeParams.AddSetParameter("DP", (float) transition.DP, (float) transition.DP, 0, out s);
massRangeParams.AddSetParameter("CE", (float) transition.CE, (float) transition.CE, 0, out s);
if (templateCxpParameterIdx > 0 && templateCxp != null)
massRangeParams.AddSetParameter("CXP", templateCxp.startVal, templateCxp.stopVal, templateCxp.stepVal, out s);
if (templateSvParameterIdx > 0 && templateSv != null)
massRangeParams.AddSetParameter("SV", templateSv.startVal, templateSv.stopVal, templateSv.stepVal, out s);
if(transition.CoV.HasValue)
massRangeParams.AddSetParameter("COV", (float)transition.CoV, (float)transition.CoV, 0, out s);
if (analystSupportsEnhancedScheduledMrm)
{
var msMassRange4 = (IMassRange4)msMassRange;
var groupId = transition.Group;
msMassRange4.GroupID = groupId;
msMassRange4.IsPrimary = transition.Primary.HasValue && transition.Primary.Value == 2 ? 0 : 1;
msMassRange4.TriggerThreshold = triggerThreshold.HasValue ? triggerThreshold.Value : Properties.Settings.Default.MinTriggerThreshold;
double? detectionWindow = transitions.Transitions.Where(t => t.Group == groupId).Max(t => t.VariableRtWindow);
msMassRange4.DetectionWindow = detectionWindow.HasValue ? detectionWindow.Value * 60 : msMassRange4.DetectionWindow;
if (medianArea.HasValue && minArea.HasValue && minArea != medianArea && transition.AveragePeakArea.HasValue && transition.AveragePeakArea < medianArea)
{
double averageArea = transition.AveragePeakArea >= 1 ? (double)transition.AveragePeakArea : 1.0;
double scaledArea = (Math.Log(averageArea - minArea.Value + 1) / Math.Log((double)medianArea))
* (Properties.Settings.Default.MaxDwellWeightingForTargets - Properties.Settings.Default.MinDwellWeightingForTargets);
msMassRange4.DwellWeighting = Properties.Settings.Default.MaxDwellWeightingForTargets - scaledArea;
}
else
{
msMassRange4.DwellWeighting = 1.0;
}
}
}
acqMethod.SaveAcqMethodToFile(transitions.OutputMethod, 1);
}
