/// <summary>
/// Overload to handle all available scans allowing for Ms1 inclusion of before + after
/// </summary>
/// <param name="AllScans"></param>
/// <param name="DependentScan"></param>
/// <param name="Number_Of_Scans_To_Average"></param>
public static void Run(ref List <Scan> scans, MonocleOptions Options)
{
foreach (Scan scan in scans)
{
if (scan.MsOrder != Options.MS_Level)
{
continue;
}
if (scan.PrecursorMasterScanNumber <= 0)
{
Console.WriteLine(String.Format("Scan {0} does not have a precursor scan number assigned.", scan.ScanNumber));
continue;
}
Scan precursorScan = scans[scan.PrecursorMasterScanNumber - 1];
var nearbyScans = GetNearbyScans(ref scans, precursorScan, Options);
// For low-res scans, or if ForceCharges is true, generate precursors with
// a range of charges given by the ChargeRangeUnknown option.
bool lowResPrecursor = precursorScan.FilterLine.Contains("ITMS");
if (lowResPrecursor || Options.ForceCharges)
{
int range = 1 + Options.ChargeRangeUnknown.High - Options.ChargeRangeUnknown.Low;
var precursors = new List <Precursor>(range);
foreach (var precursor in scan.Precursors)
{
for (int z = Options.ChargeRangeUnknown.Low; z <= Options.ChargeRangeUnknown.High; ++z)
{
var p = new Precursor(precursor);
p.Charge = z;
precursors.Add(p);
}
}
scan.Precursors = precursors;
}
if (!Options.SkipMono && !lowResPrecursor)
{
foreach (var precursor in scan.Precursors)
{
if (!Options.Charge_Detection && precursor.Charge == 0)
{
Console.WriteLine(String.Format("Scan {0} does not have a charge state assigned. Charge detection enabled.", scan.ScanNumber));
}
Run(nearbyScans, precursorScan, precursor, Options);
}
}
}
}
/// <summary>
/// Gets nearby MS1 scans around the scan given by precursorScan.
/// The window is provided as an opton, but it
/// should at least return the precursor scan.
/// </summary>
/// <param name="scans">The List of scans to filter</param>
/// <param name="precursorScan">the target scan.</param>
/// <param name="Options">Options for selecting scans.</param>
/// <returns>A list of filtered scans.</returns>
public static List <Scan> GetNearbyScans(ref List <Scan> scans, Scan precursorScan, MonocleOptions Options)
{
int window = Options.Number_Of_Scans_To_Average;
var output = new List <Scan>(window * 2);
int index = precursorScan.ScanNumber - 1;
int scanCount = 0;
if (Options.AveragingVector == AveragingVector.Before || Options.AveragingVector == AveragingVector.Both)
{
// Reel backward.
for (; index > 0 && scanCount < window; --index)
{
if (IncludeNearbyScan(scans[index], precursorScan))
{
++scanCount;
}
}
}
scanCount = 0;
// Collect scans.
for (; index < scans.Count && scanCount < window; ++index)
{
var scan = scans[index];
if (IncludeNearbyScan(scan, precursorScan))
{
if (scan.ScanNumber > precursorScan.ScanNumber)
{
if (Options.AveragingVector == AveragingVector.Before)
{
break;
}
++scanCount;
}
output.Add(scan);
}
}
return(output);
}
/// <summary>
/// Run a single Monocle scan.
/// </summary>
/// <param name="Ms1ScansCentroids"></param>
/// <param name="ParentScan"></param>
/// <param name="precursor"></param>
public static void Run(List <Scan> Ms1ScansCentroids, Scan ParentScan, Precursor precursor, MonocleOptions Options)
{
double precursorMz = precursor.IsolationMz;
if (precursorMz < 1)
{
precursorMz = precursor.Mz;
}
int precursorCharge = precursor.Charge;
if (Options.UseMostIntense && precursor.IsolationWidth > 0)
{
// Re-assign the precursor m/z to that of the most intense peak in the isolation window.
int peakIndex = PeakMatcher.MostIntenseIndex(ParentScan, precursor.IsolationMz, precursor.IsolationWidth / 2, PeakMatcher.DALTON);
if (peakIndex >= 0)
{
precursorMz = ParentScan.Centroids[peakIndex].Mz;
}
}
// Search for ion in parent scan, use parent ion mz for future peaks
int index = PeakMatcher.Match(ParentScan, precursorMz, 50, PeakMatcher.PPM);
if (index >= 0)
{
precursorMz = ParentScan.Centroids[index].Mz;
}
// For charge detection
int bestCharge = 0;
double bestScore = -1;
int bestIndex = 0;
List <double> bestPeaks = new List <double>();
List <double> bestPeakIntensities = new List <double>();
//Create new class to maintain ref class options
ChargeRange chargeRange = new ChargeRange(precursorCharge, precursorCharge);
if (Options.Charge_Detection || precursorCharge == 0)
{
chargeRange.Low = Options.Charge_Range.Low;
chargeRange.High = Options.Charge_Range.High;
}
for (int charge = chargeRange.Low; charge <= chargeRange.High; charge++)
{
// Restrict number of isotopes to consider based on precursor mass.
double mass = precursor.Mz * charge;
var isotopeRange = new IsotopeRange(mass);
// Generate expected relative intensities.
List <double> expected = PeptideEnvelopeCalculator.GetTheoreticalEnvelope(precursorMz, charge, isotopeRange.CompareSize);
Vector.Scale(expected);
PeptideEnvelope envelope = PeptideEnvelopeExtractor.Extract(Ms1ScansCentroids, precursorMz, charge, isotopeRange.Left, isotopeRange.Isotopes);
// Get best match using dot product.
// Limit the number of isotopeRange peaks to test
for (int i = 0; i < (isotopeRange.Isotopes - (isotopeRange.CompareSize - 1)); ++i)
{
List <double> observed = envelope.averageIntensity.GetRange(i, expected.Count);
Vector.Scale(observed);
PeptideEnvelopeExtractor.ScaleByPeakCount(observed, envelope, i);
double score = Vector.Dot(observed, expected);
// add 5% to give bias toward left peaks.
if (score > bestScore * 1.05)
{
bestScore = score;
if (score > 0.1)
{
// A peak to the left is included, so add
// offset to get monoisotopic index.
bestIndex = i + 1;
bestCharge = charge;
bestPeaks = envelope.mzs[bestIndex];
bestPeakIntensities = envelope.intensities[bestIndex];
}
}
}
} // end charge for loop
if (bestCharge > 0)
{
precursor.Charge = bestCharge;
}
// Calculate m/z
if (bestPeaks.Count > 0)
{
precursor.Mz = Vector.WeightedAverage(bestPeaks, bestPeakIntensities);
}
else
{
precursor.Mz = precursorMz;
}
precursor.IsolationSpecificity = IsolationSpecificityCalculator.calculate(
ParentScan.Centroids,
precursor.IsolationMz,
precursor.Mz,
precursor.Charge,
precursor.IsolationWidth
);
}
/// <summary>
/// Overload to handle all available scans allowing for Ms1 inclusion of before + after
/// </summary>
/// <param name="AllScans"></param>
/// <param name="DependentScan"></param>
/// <param name="Number_Of_Scans_To_Average"></param>
public static void Run(ref List <Scan> scans, MonocleOptions Options)
{
if (Options.Ms2Ms3Precursor)
{
AssignMs3Precursors(scans);
}
CheckMs2Precursors(scans);
foreach (Scan scan in scans)
{
if (scan.MsOrder != Options.MS_Level)
{
continue;
}
if (scan.PrecursorMasterScanNumber <= 0)
{
Console.WriteLine(String.Format("Scan {0} does not have a precursor scan number assigned.", scan.ScanNumber));
continue;
}
Scan precursorScan = scans[scan.PrecursorMasterScanNumber - 1];
// For low-res scans, or if ForceCharges is true, or if there's no charge information
// and monoisotopic peak detection is disabled, generate precursors with
// a range of charges given by the ChargeRangeUnknown option.
bool lowResPrecursor = precursorScan.FilterLine.Contains("ITMS");
int range = 1 + Options.ChargeRangeUnknown.High - Options.ChargeRangeUnknown.Low;
var precursors = new List <Precursor>(range);
foreach (var precursor in scan.Precursors)
{
if (lowResPrecursor || Options.ForceCharges || (precursor.Charge == 0 && Options.SkipMono))
{
for (int z = Options.ChargeRangeUnknown.Low; z <= Options.ChargeRangeUnknown.High; ++z)
{
var p = new Precursor(precursor);
p.Charge = z;
precursors.Add(p);
}
}
}
if (precursors.Count > 0)
{
scan.Precursors = precursors;
}
if (!Options.SkipMono && !lowResPrecursor)
{
var nearbyScans = GetNearbyScans(ref scans, precursorScan, Options);
precursors = new List <Precursor>();
foreach (var precursor in scan.Precursors)
{
if (!Options.Charge_Detection && precursor.Charge == 0)
{
// Charge detection will be enabled in the Run method.
Console.WriteLine(String.Format("Scan {0} does not have a charge state assigned. Charge detection enabled.", scan.ScanNumber));
}
Run(nearbyScans, precursorScan, precursor, Options);
// If there is still no charge, use charge range.
if (precursor.Charge == 0)
{
Console.WriteLine(String.Format("No charge found for scan {0}. Using charge range.", scan.ScanNumber));
for (int z = Options.ChargeRangeUnknown.Low; z <= Options.ChargeRangeUnknown.High; ++z)
{
var p = new Precursor(precursor);
p.Charge = z;
precursors.Add(p);
}
}
else
{
precursors.Add(precursor);
}
}
scan.Precursors = precursors;
}
}
}
