private void TestTargetedMsmsCommon(string templateFilePath, string methodFilePath, bool doTOFMs)
{
var method = GetMethod(methodFilePath);
Assert.AreEqual(1, method.PeriodCount);
var period = (Period)method.GetPeriod(0);
// Read in the template method for comparison
MassSpecMethod templateMethod = GetMethod(templateFilePath);
var prodIonIndex = ((Period)templateMethod.GetPeriod(0)).ExperimCount == 1 ? 0 : 1;
var templateProdIonExpt = (Experiment)((Period)(templateMethod.GetPeriod(0))).GetExperiment(prodIonIndex);
var templateTofMsExpt = ((Period)templateMethod.GetPeriod(0)).ExperimCount == 2
? (Experiment)((Period)(templateMethod.GetPeriod(0))).GetExperiment(0)
: null;
if (doTOFMs)
{
// We should have 1 "TOF MS" experiments and 20 "Product Ion" experiments
Assert.AreEqual(21, period.ExperimCount);
// first experiment should be a TOF experiment
var experiment = (Experiment)period.GetExperiment(0);
Assert.AreEqual(BuildAnalystFullScanMethod.TOF_MS_SCAN, experiment.ScanType);
if (templateTofMsExpt != null)
{
CompareExperiments(templateTofMsExpt, experiment, IsQstarTemplate(templateFilePath));
}
experiment = (Experiment)period.GetExperiment(1);
Assert.AreEqual(BuildAnalystFullScanMethod.PROD_ION_SCAN, experiment.ScanType);
CompareExperiments(templateProdIonExpt, experiment, IsQstarTemplate(templateFilePath));
}
else
{
// We should have 20 "Product Ion" experiments
Assert.AreEqual(20, period.ExperimCount);
var experiment = (Experiment)period.GetExperiment(0);
Assert.AreEqual(BuildAnalystFullScanMethod.PROD_ION_SCAN, experiment.ScanType);
CompareExperiments(templateProdIonExpt, experiment, IsQstarTemplate(templateFilePath));
}
}
public void TestMRMMethod()
{
string projectDirectory = GetProjectDirectory();
var args = new[] { Path.Combine(projectDirectory, METHOD_FILE),
Path.Combine(projectDirectory, LIST_UNSCHED) };
var builder = new BuildQtrapMethod();
builder.ParseCommandArgs(args);
builder.build();
string methodFilePath = Path.GetFullPath(Path.Combine(projectDirectory, METHOD_UNSCHED));
// read the updated method and make sure that the
// transition list has been included
MassSpecMethod method = GetMethod(methodFilePath);
var period = (Period)method.GetPeriod(0);
var msExperiment = (Experiment)period.GetExperiment(0);
Assert.AreEqual(60, msExperiment.MassRangesCount);
// Check the first one
// 744.839753,1087.49894,20,APR.AGLCQTFVYGGCR.y9.light,85.4,38.2
var massRange = (MassRange)msExperiment.GetMassRange(0);
Assert.AreEqual(20, massRange.DwellTime);
Assert.AreEqual(744.839753, massRange.QstartMass, 0.00005);
Assert.AreEqual(0, massRange.QstopMass);
Assert.AreEqual(1087.49894, massRange.QstepMass, 0.00005);
var msMassRange3 = (IMassRange3)massRange;
Assert.AreEqual("APR.AGLCQTFVYGGCR.y9.light", msMassRange3.CompoundID);
// Check the last one
// 572.791863,724.375566,20,CRP.GYSIFSYATK.y6.heavy,72.6,28.2
massRange = (MassRange)msExperiment.GetMassRange(59);
Assert.AreEqual(20, massRange.DwellTime);
Assert.AreEqual(572.791863, massRange.QstartMass, 0.00005);
Assert.AreEqual(0, massRange.QstopMass);
Assert.AreEqual(724.375566, massRange.QstepMass, 0.00005);
msMassRange3 = (IMassRange3)massRange;
Assert.AreEqual("CRP.GYSIFSYATK.y6.heavy", msMassRange3.CompoundID);
DeleteOutput(methodFilePath);
}
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);
}
private void ValidateMethod(MassSpecMethod method)
{
// Do some validation that happens regardless of instrument
if (method == null)
{
throw new IOException(string.Format("Failed to open template method {0}. " +
"The given template may be invalid for the available version of Analyst.",
TemplateMethod));
}
if (method.PeriodCount == 0)
{
throw new IOException(string.Format("Invalid template method {0}. Expecting at least one period.",
TemplateMethod));
}
// Get the last period in the given template method.
// We will add transitions to the last period only.
var msPeriod = (Period)method.GetPeriod(method.PeriodCount - 1);
var msExperiment = (Experiment)msPeriod.GetExperiment(0);
var experimentType = msExperiment.ScanType;
if (experimentType != 4)
{
throw new IOException(string.Format("Invalid template method {0}. Experiment type must be MRM.",
TemplateMethod));
}
var msExperiment7 = (IExperiment7)msExperiment;
if (RTWindowInSeconds.HasValue)
{
msExperiment7.LCPeakWidth = RTWindowInSeconds.Value;
msExperiment7.KnownRetentionTimes = 1;
}
else
{
msExperiment7.KnownRetentionTimes = 0;
}
}
private static bool IsDataDependentMethod(MassSpecMethod method)
{
return(((IMassSpecMethod2)method).DataDependent == 1);
}
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;
}
}
}
private void ValidateMethod(MassSpecMethod method)
{
if (method == null)
{
throw new IOException(string.Format("Failed to open template method {0}. " +
"The given template may be invalid for the available version of Analyst.",
TemplateMethod));
}
if (method.PeriodCount != 1)
{
throw new IOException(string.Format("Invalid template method {0}. Expecting only one period.",
TemplateMethod));
}
var period = (Period)method.GetPeriod(0);
var experimentCount = period.ExperimCount;
if (InclusionList || ScheduledMethod)
{
if (!IsDataDependentMethod(method))
{
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. " +
"Template does not support inclusion lists.",
TemplateMethod));
}
// A valid IDA method will have at least one TOF MS scan and one Product Ion scan
// On the 5600 (Analyst TF1.5)we can have 1 or 2 TOF MS scans followed by 1 Product Ion scan
// On the QSTAR (Analyst 2.0) we should have 1 TOF MS scan followed by 1 or more Product Ion scans
if (experimentCount < 2)
{
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. " +
"Template must have one or two TOF MS experiments and at least one Product Ion experiment.",
TemplateMethod));
}
// get the first experiment, it should be a TOF MS experiment
var msExperiment = (Experiment)period.GetExperiment(0);
if (!IsTofMsScan(msExperiment))
{
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. " +
"First experiment type must be TOF MS.",
TemplateMethod));
}
// get the last experiment, it should be a Product ion experiment
msExperiment = ((Experiment)period.GetExperiment(experimentCount - 1));
if (!IsProductIonScan(msExperiment))
{
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. " +
"Last experiment type must be Product Ion Scan.",
TemplateMethod));
}
}
else
{
if (IsDataDependentMethod(method))
{
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. " +
"The given template is for a data dependent experiment.",
TemplateMethod));
}
if (experimentCount != 1 && experimentCount != 2)
{
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. " +
"Template must have 1 or 2 experiments.",
TemplateMethod));
}
// If the template has 1 experiment it should be a Product Ion experiment
if (experimentCount == 1)
{
var msExperiment = (Experiment)period.GetExperiment(0);
if (!IsProductIonScan(msExperiment))
{
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. " +
"Template does not have a Product Ion Scan.",
TemplateMethod));
}
}
// If the template has 2 experiments require the first one to be a TOF MS and the second one to be a Product Ion
if (experimentCount == 2)
{
var msExperiment = (Experiment)period.GetExperiment(0);
if (!IsTofMsScan(msExperiment))
{
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. " +
"Template has 2 experiments. First experiment type must be TOF MS.",
TemplateMethod));
}
msExperiment = (Experiment)period.GetExperiment(1);
if (!IsProductIonScan(msExperiment))
{
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. " +
"Template has 2 experiments. Second experiment type must be Product Ion Scan.",
TemplateMethod));
}
}
}
}
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;
}
}
}
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 ValidateMethod(MassSpecMethod method)
{
if (method == null)
{
throw new IOException(string.Format("Failed to open template method {0}. " +
"The given template may be invalid for the available version of Analyst.",
TemplateMethod));
}
if (method.PeriodCount != 1)
{
throw new IOException(string.Format("Invalid template method {0}. Expecting only one period.",
TemplateMethod));
}
var period = (Period) method.GetPeriod(0);
var experimentCount = period.ExperimCount;
if (InclusionList || ScheduledMethod)
{
if(!IsDataDependentMethod(method))
{
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. "+
"Template does not support inclusion lists.",
TemplateMethod));
}
// A valid IDA method will have at least one TOF MS scan and one Product Ion scan
// On the 5600 (Analyst TF1.5)we can have 1 or 2 TOF MS scans followed by 1 Product Ion scan
// On the QSTAR (Analyst 2.0) we should have 1 TOF MS scan followed by 1 or more Product Ion scans
if (experimentCount < 2)
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. " +
"Template must have one or two TOF MS experiments and at least one Product Ion experiment.",
TemplateMethod));
// get the first experiment, it should be a TOF MS experiment
var msExperiment = (Experiment) period.GetExperiment(0);
if (!IsTofMsScan(msExperiment))
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. " +
"First experiment type must be TOF MS.",
TemplateMethod));
// get the last experiment, it should be a Product ion experiment
msExperiment = ((Experiment)period.GetExperiment(experimentCount -1));
if (!IsProductIonScan(msExperiment))
throw new IOException(string.Format("Invalid template method for an IDA or Scheduled experiment {0}. " +
"Last experiment type must be Product Ion Scan.",
TemplateMethod));
}
else
{
if (IsDataDependentMethod(method))
{
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. "+
"The given template is for a data dependent experiment.",
TemplateMethod));
}
if (experimentCount != 1 && experimentCount != 2)
{
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. " +
"Template must have 1 or 2 experiments.",
TemplateMethod));
}
// If the template has 1 experiment it should be a Product Ion experiment
if(experimentCount == 1)
{
var msExperiment = (Experiment)period.GetExperiment(0);
if (!IsProductIonScan(msExperiment))
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. "+
"Template does not have a Product Ion Scan.",
TemplateMethod));
}
// If the template has 2 experiments require the first one to be a TOF MS and the second one to be a Product Ion
if(experimentCount == 2)
{
var msExperiment = (Experiment)period.GetExperiment(0);
if (!IsTofMsScan(msExperiment))
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. "+
"Template has 2 experiments. First experiment type must be TOF MS.",
TemplateMethod));
msExperiment = (Experiment)period.GetExperiment(1);
if (!IsProductIonScan(msExperiment))
throw new IOException(string.Format("Invalid template method for a targeted MS/MS experiment {0}. "+
"Template has 2 experiments. Second experiment type must be Product Ion Scan.",
TemplateMethod));
}
}
}
private static bool IsDataDependentMethod(MassSpecMethod method)
{
return ((IMassSpecMethod2) method).DataDependent == 1;
}
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;
}
private void ValidateMethod(MassSpecMethod method)
{
// Do some validation that happens regardless of instrument
if (method == null)
{
throw new IOException(string.Format("Failed to open template method {0}. " +
"The given template may be invalid for the available version of Analyst.",
TemplateMethod));
}
if (method.PeriodCount == 0)
{
throw new IOException(string.Format("Invalid template method {0}. Expecting at least one period.",
TemplateMethod));
}
// Get the last period in the given template method.
// We will add transitions to the last period only.
var msPeriod = (Period)method.GetPeriod(method.PeriodCount - 1);
var msExperiment = (Experiment)msPeriod.GetExperiment(0);
var experimentType = msExperiment.ScanType;
if (experimentType != 4)
{
throw new IOException(string.Format("Invalid template method {0}. Experiment type must be MRM.",
TemplateMethod));
}
var msExperiment7 = (IExperiment7)msExperiment;
if (RTWindowInSeconds.HasValue)
{
msExperiment7.LCPeakWidth = RTWindowInSeconds.Value;
msExperiment7.KnownRetentionTimes = 1;
}
else
{
msExperiment7.KnownRetentionTimes = 0;
}
}
// read the updated method and make sure that the inclusion list is in the method
private void TestIDACommon(string methodFilePath, bool isScheduled)
{
MassSpecMethod myMethod = GetMethod(methodFilePath);
// The method should have an inclusion list
object idaServer;
((IMassSpecMethod2)myMethod).GetDataDependSvr(out idaServer);
var useInclusionList = 0;
((IDDEMethodObj)idaServer).getUseIncludeList(ref useInclusionList);
Assert.AreEqual(1, useInclusionList);
// The inclusion list should have 20 entries.
int inclusionListSize = 0;
((IDDEMethodObj)idaServer).GetIonListSize(1, ref inclusionListSize);
Assert.AreEqual(20, inclusionListSize);
// test m/z for the first entry in the inclusion list
double mz = 0;
((IDDEMethodObj)idaServer).GetIncludeIonEntry(0, ref mz);
Assert.AreEqual(744.839753, mz);
// test m/z the last entry in the inclusion list
((IDDEMethodObj)idaServer).GetIncludeIonEntry(19, ref mz);
Assert.AreEqual(572.791863, mz);
// test retention time
if (isScheduled)
{
// Since this is an scheduled method, the retention time of each entry should be a non-zero value
double rt = -1;
((IDDEMethodObj3)idaServer).GetIncludeRetTimeEntry(0, ref rt);
Assert.AreEqual(19.49, rt);
((IDDEMethodObj3)idaServer).GetIncludeRetTimeEntry(19, ref rt);
Assert.AreEqual(20.48, rt);
double exceedCountSwitch = -1;
((IDDEMethodObj)idaServer).getExceedCountSwitch(ref exceedCountSwitch);
Assert.AreEqual(2000000, exceedCountSwitch);
double intensityThreshold = -1;
((IDDEMethodObj)idaServer).getIntensityThreshold(ref intensityThreshold);
Assert.AreEqual(0, intensityThreshold);
int spectraSwicth = -1;
((IDDEMethodObj)idaServer).getSpectraSwitch(ref spectraSwicth);
Assert.AreEqual(12, spectraSwicth);
}
else
{
// Since this is an unscheduled method the retention time of each entry should
// be set to 0
double rt = -1;
((IDDEMethodObj3)idaServer).GetIncludeRetTimeEntry(0, ref rt);
Assert.AreEqual(0, rt);
((IDDEMethodObj3)idaServer).GetIncludeRetTimeEntry(19, ref rt);
Assert.AreEqual(0, rt);
}
DeleteOutput(methodFilePath);
}
