private void Orbitrap_MsScanArrived(object sender, MsScanEventArgs e)
{
string accessId;
using (IMsScan scan = (IMsScan)e.GetScan()) // caution! You must dispose this, or you block shared memory!
{
// The access ID gives a feedback about placed scans or scans generated by the instrument.
scan.SpecificInformation.TryGetValue("Access Id:", out accessId);
Console.WriteLine("{0:HH:mm:ss,fff} scan {1} arrived", DateTime.Now, accessId);
////// The common part is shared by all Thermo Fisher instruments, these settings mainly form the so called filter string
////// which also appears on top of each spectrum in many visualizers.
//Console.WriteLine("----------------Common--------------");
//Dump("Common", scan.CommonInformation);
////// The specific part is individual for each instrument type. Many values are shared by different Exactive Series models.
//Console.WriteLine("----------------Specific--------------");
// Dump("Specific", scan.SpecificInformation);
//Dump(scan);
var ib = IsBoxCarScan(scan);
Console.WriteLine("IsBoxCar Scan: {0}", ib);
FullScan.PlaceFullScan(m_scans, Parameters);
//List<double> dynamicBoxCarRange = new List<double> { 600, 700, 800, 900, 1000 };
//BoxCarScan.PlaceBoxCarScan(m_scans, Parameters, dynamicBoxCarRange);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, 750);
BoxCarScan.PlaceStaticBoxCarScan(m_scans, Parameters);
}
}
private void PlaceBU_MS2Scan(IMsScan scan, List <IsoEnvelop> isoEnvelops)
{
Console.WriteLine("\n{0:HH:mm:ss,fff} Deconvolute Dynamic BoxCar Start", DateTime.Now);
int placeScanCount = 0;
foreach (var iso in isoEnvelops.OrderByDescending(p => p.TotalIntensity))
{
if (placeScanCount >= Parameters.MS1IonSelecting.TopN)
{
break;
}
if (DynamicExclusionList.isNotInExclusionList(iso.ExperimentIsoEnvelop.First().Mz, Parameters.MS1IonSelecting.ExclusionTolerance))
{
var dataTime = DateTime.Now;
lock (lockerExclude)
{
DynamicExclusionList.exclusionList.Enqueue(new Tuple <double, int, DateTime>(iso.ExperimentIsoEnvelop.First().Mz, iso.Charge, dataTime));
Console.WriteLine("2 ExclusionList Enqueue: {0}", iso.ExperimentIsoEnvelop.First().Mz);
}
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, iso.ExperimentIsoEnvelop.First().Mz);
placeScanCount++;
}
}
}
private void PlaceUserDefined(IMsScan scan)
{
Console.WriteLine("\n{0:HH:mm:ss,fff} UserDefined Start", DateTime.Now);
var monomass = 16950.88339;
Dictionary <int, double> mz_z = new Dictionary <int, double>();
for (int i = 15; i <= 27; i++)
{
mz_z.Add(i, monomass.ToMz(i));
}
var mzs = mz_z.Values;
//foreach (var mz in mzs)
//{
// Parameters.MS2ScanSetting.NCE = 10;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 15;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 20;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 25;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 30;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 35;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 40;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 45;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE = 50;
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
//}
//Parameters.MS2ScanSetting.NCE = 25;
//foreach (var mz in mzs)
//{
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
// DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
// Parameters.MS2ScanSetting.NCE_factors = "null";
//}
int j = 15;
while (j <= 27)
{
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz_z[j]);
Parameters.MS2ScanSetting.NCE_factors = "null";
j += 1;
}
List <double> comb = new List <double>();
comb.Add(mz_z[20]);
comb.Add(mz_z[21]);
comb.Add(mz_z[22]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
comb.Clear();
comb.Add(mz_z[19]);
comb.Add(mz_z[21]);
comb.Add(mz_z[23]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
comb.Clear();
comb.Add(mz_z[17]);
comb.Add(mz_z[21]);
comb.Add(mz_z[25]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
comb.Clear();
comb.Add(mz_z[17]);
comb.Add(mz_z[19]);
comb.Add(mz_z[21]);
comb.Add(mz_z[23]);
comb.Add(mz_z[25]);
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.9, 1, 1.1]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.8, 1, 1.2]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "[0.6, 1, 1.4]";
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, comb);
Parameters.MS2ScanSetting.NCE_factors = "null";
FullScan.PlaceFullScan(m_scans, Parameters);
}
private void PlaceDynamicBoxCarMS2Scan(IMsScan scan, List <ChargeEnvelop> chargeEnvelops, List <IsoEnvelop> isoEnvelops)
{
Console.WriteLine("\n{0:HH:mm:ss,fff} Deconvolute Dynamic BoxCar Start", DateTime.Now);
int placeScanCount = 0;
foreach (var ce in chargeEnvelops)
{
if (placeScanCount >= Parameters.MS1IonSelecting.TopN)
{
return;
}
var mzs = ce.distributions.Select(p => p.mz).OrderBy(p => p).ToArray();
int matchedCount = DynamicDBCExclusionList.MatchExclusionList(mzs, 0.1);
if (matchedCount == 0)
{
Console.WriteLine("DynamicDBCExclusionList didn't match.");
if (Parameters.BoxCarScanSetting.DoDbcForMS2)
{
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, ce.mzs_box);
}
else
{
var mz = ce.distributions_withIso.OrderByDescending(p => p.intensity).First().isoEnvelop.ExperimentIsoEnvelop.First().Mz;
if (DynamicExclusionList.isNotInExclusionList(mz, Parameters.MS1IonSelecting.ExclusionTolerance))
{
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, mz);
}
}
placeScanCount++;
lock (lockerExclude)
{
DynamicDBCExclusionList.DBCExclusionList.Enqueue(new DynamicDBCValue(mzs, 0, DateTime.Now));
foreach (var x in ce.distributions_withIso)
{
var mz = x.isoEnvelop.ExperimentIsoEnvelop.First().Mz;
if (DynamicExclusionList.isNotInExclusionList(mz, Parameters.MS1IonSelecting.ExclusionTolerance))
{
DynamicExclusionList.exclusionList.Enqueue(new Tuple <double, int, DateTime>(mz, x.charge, DateTime.Now));
Console.WriteLine("1 ExclusionList Enqueue: {0}", mz);
}
}
}
}
else
{
Console.WriteLine("DynamicDBCExclusionList did match.");
}
}
if (placeScanCount >= Parameters.MS1IonSelecting.TopN)
{
return;
}
foreach (var iso in isoEnvelops)
{
if (placeScanCount >= Parameters.MS1IonSelecting.TopN)
{
return;
}
if (DynamicExclusionList.isNotInExclusionList(iso.ExperimentIsoEnvelop.First().Mz, Parameters.MS1IonSelecting.ExclusionTolerance))
{
var dataTime = DateTime.Now;
lock (lockerExclude)
{
DynamicExclusionList.exclusionList.Enqueue(new Tuple <double, int, DateTime>(iso.ExperimentIsoEnvelop.First().Mz, iso.Charge, dataTime));
Console.WriteLine("2 ExclusionList Enqueue: {0}", iso.ExperimentIsoEnvelop.First().Mz);
}
DataDependentScan.PlaceMS2Scan(m_scans, Parameters, iso.ExperimentIsoEnvelop.First().Mz);
placeScanCount++;
}
}
}
