private void WriteToTargetedMSMSTemplate(MassSpecMethod method, MethodTransitions transitions)
{
var period = (Period)method.GetPeriod(0);
Experiment tofExperiment = null;
Experiment prodIonExperiment;
switch (period.ExperimCount)
{
case 2:
tofExperiment = (Experiment) period.GetExperiment(0);
prodIonExperiment = (Experiment) period.GetExperiment(1);
// delete the product ion experiment. We will be adding one for each precursor ion in the transition list.
period.DeleteExperiment(1);
break;
case 1:
prodIonExperiment = (Experiment)period.GetExperiment(0);
// delete the product ion experiment. We will be adding one for each precursor ion in the transition list.
period.DeleteExperiment(0);
break;
default:
throw new IOException(string.Format("Expected 1 or 2 experiments in the template. Found {0} experiments.", period.ExperimCount));
}
int j;
if (Ms1Scan)
{
// If the template does not already have a TOF MS scan add one now.
if(tofExperiment == null)
{
var experiment = (Experiment)period.CreateExperiment(out j);
experiment.InitExperiment();
experiment.ScanType = TOF_MS_SCAN;
}
}
if(prodIonExperiment == null)
{
throw new IOException("Product Ion scan was not found in the method.");
}
// Get the TOF mass range from the template
var tofPropertiesTemplate = (ITOFProperties)prodIonExperiment;
short s;
//Get initial source parameters from the template
var sourceParamsTblInput = (ParamDataColl)prodIonExperiment.SourceParamsTbl;
ParameterData param = (ParameterData) sourceParamsTblInput.FindParameter("GS1", out s);
float sourceGas1 = param == null ? 0 : param.startVal;
param = (ParameterData)sourceParamsTblInput.FindParameter("GS2", out s);
float sourceGas2 = param == null ? 0 : param.startVal;
param = (ParameterData)sourceParamsTblInput.FindParameter("CUR", out s);
float curtainGas = param == null ? 0 : param.startVal;
param = (ParameterData)sourceParamsTblInput.FindParameter("TEM", out s);
float temperature = param == null ? 0 : param.startVal;
param = (ParameterData)sourceParamsTblInput.FindParameter("IHT", out s);
float nanoTemperature = param == null ? 0 : param.startVal;
string ionSprayVoltageParamName = "ISVF"; // ISVF on 5600, IS on QSTAR
float ionSprayVoltage;
var paramData = ((ParameterData)sourceParamsTblInput.FindParameter(ionSprayVoltageParamName, out s));
if (s != -1)
{
ionSprayVoltage = paramData.startVal;
}
else
{
ionSprayVoltageParamName = "IS";
ionSprayVoltage = ((ParameterData)sourceParamsTblInput.FindParameter(ionSprayVoltageParamName, out s)).startVal;
}
// We will use parameters from the first mass range in the template product ion experiment.
var massRangeTemplate = (IMassRange)prodIonExperiment.GetMassRange(0);
var paramTblTemplate = (ParamDataColl)massRangeTemplate.MassDepParamTbl;
double minPrecursorMass = double.MaxValue;
double maxPrecursorMass = 0;
var precursorsToExperimentIndex = new Dictionary<double, int>();
foreach (var transition in transitions.Transitions)
{
if (precursorsToExperimentIndex.ContainsKey(transition.PrecursorMz))
{
transition.ExperimentIndex = IsPrecursorTypeTransition(transition)
? 0
: precursorsToExperimentIndex[transition.PrecursorMz];
continue;
}
var experiment = (Experiment) period.CreateExperiment(out j);
precursorsToExperimentIndex.Add(transition.PrecursorMz, j);
transition.ExperimentIndex = IsPrecursorTypeTransition(transition) ? 0 : j;
experiment.InitExperiment();
// Setting ScanType to 6 for QSTAR causes method export to fail. Setting it to 9 works for both AB 5600 and QSTAR
experiment.ScanType = PROD_ION_SCAN;
experiment.FixedMass = transition.PrecursorMz;
minPrecursorMass = Math.Min(minPrecursorMass, transition.PrecursorMz);
maxPrecursorMass = Math.Max(maxPrecursorMass, transition.PrecursorMz);
var tofProperties = (ITOFProperties)experiment;
tofProperties.AccumTime = tofPropertiesTemplate.AccumTime;
tofProperties.TOFMassMin = tofPropertiesTemplate.TOFMassMin;
tofProperties.TOFMassMax = tofPropertiesTemplate.TOFMassMax;
// The following should trigger the "Suggest" button functionality
// of updating the Q2 transmission window.
tofProperties.UseQ1TranDefault = 1;
//tofProperties.UseTOFExtrDefault = 1; // Works without this one.
// High Sensitivity vs. High Resolution
var tofProperties2 = experiment as ITOFProperties2;
var templateTofProperties2 = prodIonExperiment as ITOFProperties2;
if (tofProperties2 != null && templateTofProperties2 != null)
{
tofProperties2.HighSensitivity = templateTofProperties2.HighSensitivity;
}
var sourceParamsTblOutput = (ParamDataColl)experiment.SourceParamsTbl;
if (sourceParamsTblInput.FindParameter("GS1", out s) != null && s != -1)
sourceParamsTblOutput.AddSetParameter("GS1", sourceGas1, sourceGas1, 0, out s);
if (sourceParamsTblInput.FindParameter("GS2", out s) != null && s != -1)
sourceParamsTblOutput.AddSetParameter("GS2", sourceGas2, sourceGas2, 0, out s);
if (sourceParamsTblInput.FindParameter("CUR", out s) != null && s != -1)
sourceParamsTblOutput.AddSetParameter("CUR", curtainGas, curtainGas, 0, out s);
if (sourceParamsTblInput.FindParameter("TEM", out s) != null && s != -1)
sourceParamsTblOutput.AddSetParameter("TEM", temperature, temperature, 0, out s);
if (sourceParamsTblInput.FindParameter("IHT", out s) != null && s != -1)
sourceParamsTblOutput.AddSetParameter("IHT", nanoTemperature, nanoTemperature, 0, out s);
if (sourceParamsTblInput.FindParameter(ionSprayVoltageParamName, out s) != null && s != -1)
sourceParamsTblOutput.AddSetParameter(ionSprayVoltageParamName, ionSprayVoltage, ionSprayVoltage, 0, out s);
// Copy the compound dependent parameters from the template
for (int i = 0; i < experiment.MassRangesCount; i++)
{
var massRange = (IMassRange)experiment.GetMassRange(i);
var massDepParams = (ParamDataColl)massRange.MassDepParamTbl;
// Declustering potential
float dp = ((ParameterData)paramTblTemplate.FindParameter("DP", out s)).startVal;
if(s != -1)
{
if (transition.DP > 0)
dp = Convert.ToSingle(transition.DP);
massDepParams.AddSetParameter("DP", dp, dp, 0, out s);
}
// Collision engergy
float ce = ((ParameterData)paramTblTemplate.FindParameter("CE", out s)).startVal;
if (s != -1)
{
if (transition.CE > 0)
ce = Convert.ToSingle(transition.CE);
massDepParams.AddSetParameter("CE", ce, ce, 0, out s);
}
// Ion release delay
float ird = ((ParameterData)paramTblTemplate.FindParameter("IRD", out s)).startVal;
if (s != -1)
{
massDepParams.AddSetParameter("IRD", ird, ird, 0, out s);
}
// Ion release width
float irw = ((ParameterData)paramTblTemplate.FindParameter("IRW", out s)).startVal;
if (s != -1)
{
massDepParams.AddSetParameter("IRW", irw, irw, 0, out s);
}
// Collision energy spread; Only on the Analyst TF 1.5.1 and TF1.5.2
paramData = ((ParameterData)paramTblTemplate.FindParameter("CES", out s));
if (s != -1)
{
massDepParams.AddSetParameter("CES", paramData.startVal, paramData.startVal, 0, out s);
}
// Focusing potential; Only on Analyst QS 2.0
paramData = ((ParameterData)paramTblTemplate.FindParameter("FP", out s));
if (s != -1)
{
massDepParams.AddSetParameter("FP", paramData.startVal, paramData.startVal, 0, out s);
}
// Declustering potential 2; Only on Analyst QS 2.0
paramData = ((ParameterData)paramTblTemplate.FindParameter("DP2", out s));
if (s != -1)
{
massDepParams.AddSetParameter("DP2", paramData.startVal, paramData.startVal, 0, out s);
}
// Collision gas; Only on Analyst QS 2.0
paramData = ((ParameterData)paramTblTemplate.FindParameter("CAD", out s));
if (s != -1)
{
massDepParams.AddSetParameter("CAD", paramData.startVal, paramData.startVal, 0, out s);
}
}
}
// Expand the mass range for the TOF MS scan if the precursor mass of any of the MS/MS experiments
// was out of the range
if(Ms1Scan)
{
var ms1TofProperties = (ITOFProperties)(period.GetExperiment(0));
ms1TofProperties.TOFMassMin = Math.Min(ms1TofProperties.TOFMassMin, minPrecursorMass);
ms1TofProperties.TOFMassMax = Math.Max(ms1TofProperties.TOFMassMax, maxPrecursorMass);
}
}
private void WriteToIDATemplate(MassSpecMethod method, MethodTransitions transitions)
{
object idaServer;
((IMassSpecMethod2)method).GetDataDependSvr(out idaServer);
ClearIncludeList(idaServer);
double minTOFMass = 0;
double maxTOFMass = 0;
((IDDEMethodObj)idaServer).getUsersSurvTOFMasses(ref minTOFMass, ref maxTOFMass);
var addedEntries = new List<string>();
var assignedCandidateMassToRT = new Dictionary<double, double>();
var entryKeyToAssignedCandidateMass = new Dictionary<string, double>();
foreach (var transition in transitions.Transitions)
{
double retentionTime = 0;
// If the ScheduledMethod flag was set assume that the Dwell time column in the
// transition list file has retention time.
if (ScheduledMethod)
retentionTime = transition.Dwell;
string entryKey = transition.PrecursorMz + retentionTime.ToString(CultureInfo.InvariantCulture);
if (addedEntries.Contains(entryKey)
|| transition.PrecursorMz <= minTOFMass
|| transition.PrecursorMz >= maxTOFMass)
continue;
var precursorMz = Math.Round(transition.PrecursorMz, 3);
while (assignedCandidateMassToRT.ContainsKey(precursorMz))
{
// Analyst does not allow duplicate masses in inclusion list
precursorMz += 0.001;
}
((IDDEMethodObj)idaServer).AddIonEntry(1, precursorMz, retentionTime);
addedEntries.Add(entryKey);
assignedCandidateMassToRT.Add(precursorMz, retentionTime);
entryKeyToAssignedCandidateMass.Add(entryKey, precursorMz);
}
if (ScheduledMethod) // calculate experiment index which is used for exporting a quantitaion method
{
((IDDEMethodObj)idaServer).putExceedCountSwitch(2000000);
((IDDEMethodObj)idaServer).putIntensityThreshold(0);
int windowInSec = RTWindowInSeconds.HasValue ? RTWindowInSeconds.Value : 60;
((IDDEMethodObj3)idaServer).putIncludeForSecs(windowInSec);
int maxConcurrentCount = MaxConcurrentCount(assignedCandidateMassToRT, windowInSec);
((IDDEMethodObj)idaServer).putSpectraSwitch(maxConcurrentCount);
var period = (Period)method.GetPeriod(0);
while (period.ExperimCount > 2)
{
period.DeleteExperiment(period.ExperimCount -1);
}
var templateExperiment = (Experiment) period.GetExperiment(1);
for (int newExperimentIdx = 1; newExperimentIdx < maxConcurrentCount; newExperimentIdx++)
{
int pIdx;
var experiment = (IClone)period.CreateExperiment(out pIdx);
experiment.CopyDataFrom(templateExperiment);
}
// sort by mass then by RT
var massRtList = assignedCandidateMassToRT.OrderBy(c => c.Value).ThenBy(c => c.Key).ToList();
foreach (var transition in transitions.Transitions)
{
double assignedCandidateMass;
var entryKey = transition.PrecursorMz + transition.Dwell.ToString(CultureInfo.InvariantCulture);
if (!entryKeyToAssignedCandidateMass.TryGetValue(entryKey, out assignedCandidateMass))
continue;
var scheduledIndex = massRtList.FindIndex(m => Math.Abs(m.Key - assignedCandidateMass) < 0.001);
transition.ExperimentIndex = IsPrecursorTypeTransition(transition)
? 0
: (scheduledIndex%maxConcurrentCount) + 1;
}
}
}
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 static void ExportMultiQuantTextMethod(MethodTransitions transitions)
{
string filePath = Path.ChangeExtension(transitions.FinalMethod, ".MultiQuant.txt");
string export = "Group Name\tName\tStart Mass - 1\tEnd Mass - 1\tExpected RT\tPeriod\tExperiment\tExtraction Type" + Environment.NewLine;
foreach (var transition in transitions.Transitions)
{
var extarctionStart = IsPrecursorTypeTransition(transition)
? transition.PrecursorMz - transition.PrecursorWindow/2
: transition.ProductMz - transition.ProductWindow/2;
var extractionEnd = IsPrecursorTypeTransition(transition)
? transition.PrecursorMz + transition.PrecursorWindow/2
: transition.ProductMz + transition.ProductWindow/2;
var nameParts = transition.Label.Split(new[] {'.'}, StringSplitOptions.RemoveEmptyEntries);
var groupName = nameParts.Length >= 2
? string.Format("{0}.{1}", nameParts[0], nameParts[1])
: transition.Label;
export += string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}",
groupName,
transition.Label,
extarctionStart,
extractionEnd,
transition.Dwell,
1,
transition.ExperimentIndex + 1,
"Scan");
export += Environment.NewLine;
}
using (var file = new StreamWriter(filePath))
{
file.Write(export);
}
}
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);
}
