public override IEnumerable <AllowedIntervalWithNotch> GetAllowedPrecursorMassIntervalsFromTheoreticalMass(double peptideMonoisotopicMass)
{
for (int j = 0; j < AcceptableSortedMassShifts.Length; j++)
{
yield return(new AllowedIntervalWithNotch(Tolerance.GetRange(peptideMonoisotopicMass + AcceptableSortedMassShifts[j]), j));
}
}
public void ToleranceNewTest()
{
var tol = new Tolerance(ToleranceUnit.Absolute, 9, 10);
Assert.AreEqual(4, tol.GetRange(5).Minimum);
Assert.AreEqual(6, tol.GetRange(5).Maximum);
}
public static double GetPValue(PSM psm, Tolerance prod_tolerance, double cutoff)
{
// Get the width of the product ion tolerance at the isolation mz;
double productToleranceWidth = prod_tolerance.GetRange(psm.IsolationMZ).Width;
double cutoffThreshold = psm.Spectrum.GetBasePeakIntensity() * cutoff;
return(Math.Min(1.0, psm.Spectrum.Count(peak => peak.Intensity >= cutoffThreshold) * 2 * productToleranceWidth / psm.ScanWidth));
}
public void TolerancePPMGetRange()
{
var tol = new Tolerance(ToleranceUnit.PPM, 1e6 - 1, 1e6);
Assert.AreEqual(20, tol.GetRange(1e7).Width);
Assert.AreEqual("±1.0000 PPM", tol.ToString());
}
public IEnumerable<Fragment> MatchFragments(IEnumerable<Fragment> fragments, Tolerance tolerance, double percentCutoff, params int[] chargeStates)
{
double basePeakInt = MassSpectrum.GetBasePeakIntensity();
double lowThreshold = basePeakInt*percentCutoff;
double summedIntensity = 0;
double totalIntensity = MassSpectrum.GetTotalIonCurrent();
foreach (Fragment fragment in fragments)
{
foreach (int chargeState in chargeStates)
{
double mz = fragment.ToMz(chargeState);
var peak = MassSpectrum.GetClosestPeak(tolerance.GetRange(mz));
if (peak != null && peak.Intensity >= lowThreshold)
{
Add(new FragmentSpectralMatch(MassSpectrum, fragment, tolerance, chargeState));
yield return fragment;
summedIntensity += peak.Intensity;
}
}
}
PercentTIC = 100.0 * summedIntensity / totalIntensity;
}
public IEnumerable <Fragment> MatchFragments(IEnumerable <Fragment> fragments, Tolerance tolerance, double percentCutoff, params int[] chargeStates)
{
double basePeakInt = Spectrum.GetBasePeakIntensity();
double lowThreshold = basePeakInt * percentCutoff;
double summedIntensity = 0;
double totalIntensity = Spectrum.GetTotalIonCurrent();
foreach (Fragment fragment in fragments)
{
foreach (int chargeState in chargeStates)
{
double mz = fragment.ToMz(chargeState);
var peak = Spectrum.GetClosestPeak(tolerance.GetRange(mz));
if (peak != null && peak.Intensity >= lowThreshold)
{
Add(new FragmentSpectralMatch(Spectrum, fragment, tolerance, chargeState));
yield return(fragment);
summedIntensity += peak.Intensity;
}
}
}
PercentTIC = 100.0 * summedIntensity / totalIntensity;
}
//private double Search(ref double[] eMasses, ref double[] eIntenisties, double[] tMasses, double productTolerance, double tic, ref Dictionary<double, double> scores)
//{
// double score = 0.0;
// int eLength = eMasses.Length;
// int tLength = tMasses.Length;
// int e = 0;
// foreach (double t in tMasses)
// {
// double storedScore;
// if (scores.TryGetValue(t, out storedScore))
// {
// score += storedScore;
// continue;
// }
// double minMZ = t - productTolerance;
// double maxMZ = t + productTolerance;
// while (e < eLength && eMasses[e] < minMZ)
// e++;
// if (e >= eLength)
// break;
// if (eMasses[e] > maxMZ)
// continue;
// double intensities = 0;
// int index = e; // switch variables to keep e the same for the next loop around
// do
// {
// intensities += eIntenisties[index];
// index++;
// } while (index < eLength && eMasses[index] < maxMZ);
// storedScore = 1 + intensities/tic;
// score += storedScore;
// scores[t] = storedScore;
// }
// return score;
//}
/// <summary>
/// The main searching algorithm of Morpheus
/// </summary>
/// <param name="eMasses">The experimental masses</param>
/// <param name="eIntenisties">The experimental intensities</param>
/// <param name="tMasses">The theoretical masses</param>
/// <param name="productTolerance">The product mass tolerance</param>
/// <param name="tic">The total ion current of the experimental peaks</param>
/// <returns></returns>
private double Search(double[] eMasses, double[] eIntenisties, double[] tMasses, Tolerance productTolerance, double tic)
{
double score = 0.0;
double intensities = 0.0;
int eLength = eMasses.Length;
int tLength = tMasses.Length;
int e = 0;
bool forceCheck = productTolerance.GetMinimumValue(tMasses[tLength - 1]) >= eMasses[eLength - 1];
if (forceCheck)
{
foreach (double t in tMasses)
{
IRange<double> range = productTolerance.GetRange(t);
double minMZ = range.Minimum;
double maxMZ = range.Maximum;
while (e < eLength && eMasses[e] < minMZ)
e++;
if (e >= eLength)
break;
if (eMasses[e] > maxMZ)
continue;
score++;
int index = e; // switch variables to keep e the same for the next loop around
do
{
intensities += eIntenisties[index];
index++;
} while (index < eLength && eMasses[index] < maxMZ);
}
}
else
{
foreach (double t in tMasses)
{
IRange<double> range = productTolerance.GetRange(t);
double minMZ = range.Minimum;
double maxMZ = range.Maximum;
while (eMasses[e] < minMZ)
e++;
if (eMasses[e] > maxMZ)
continue;
score++;
int index = e; // switch variables to keep e the same for the next loop around
do
{
intensities += eIntenisties[index];
index++;
} while (index < eLength && eMasses[index] < maxMZ);
}
}
return score + intensities/tic;
}
//private double Search(ref double[] eMasses, ref double[] eIntenisties, double[] tMasses, double productTolerance, double tic, ref Dictionary<double, double> scores)
//{
// double score = 0.0;
// int eLength = eMasses.Length;
// int tLength = tMasses.Length;
// int e = 0;
// foreach (double t in tMasses)
// {
// double storedScore;
// if (scores.TryGetValue(t, out storedScore))
// {
// score += storedScore;
// continue;
// }
// double minMZ = t - productTolerance;
// double maxMZ = t + productTolerance;
// while (e < eLength && eMasses[e] < minMZ)
// e++;
// if (e >= eLength)
// break;
// if (eMasses[e] > maxMZ)
// continue;
// double intensities = 0;
// int index = e; // switch variables to keep e the same for the next loop around
// do
// {
// intensities += eIntenisties[index];
// index++;
// } while (index < eLength && eMasses[index] < maxMZ);
// storedScore = 1 + intensities/tic;
// score += storedScore;
// scores[t] = storedScore;
// }
// return score;
//}
/// <summary>
/// The main searching algorithm of Morpheus
/// </summary>
/// <param name="eMasses">The experimental masses</param>
/// <param name="eIntenisties">The experimental intensities</param>
/// <param name="tMasses">The theoretical masses</param>
/// <param name="productTolerance">The product mass tolerance</param>
/// <param name="tic">The total ion current of the experimental peaks</param>
/// <returns></returns>
private double Search(double[] eMasses, double[] eIntenisties, double[] tMasses, Tolerance productTolerance, double tic)
{
double score = 0.0;
double intensities = 0.0;
int eLength = eMasses.Length;
int tLength = tMasses.Length;
int e = 0;
bool forceCheck = productTolerance.GetMinimumValue(tMasses[tLength - 1]) >= eMasses[eLength - 1];
if (forceCheck)
{
foreach (double t in tMasses)
{
IRange <double> range = productTolerance.GetRange(t);
double minMZ = range.Minimum;
double maxMZ = range.Maximum;
while (e < eLength && eMasses[e] < minMZ)
{
e++;
}
if (e >= eLength)
{
break;
}
if (eMasses[e] > maxMZ)
{
continue;
}
score++;
int index = e; // switch variables to keep e the same for the next loop around
do
{
intensities += eIntenisties[index];
index++;
} while (index < eLength && eMasses[index] < maxMZ);
}
}
else
{
foreach (double t in tMasses)
{
IRange <double> range = productTolerance.GetRange(t);
double minMZ = range.Minimum;
double maxMZ = range.Maximum;
while (eMasses[e] < minMZ)
{
e++;
}
if (eMasses[e] > maxMZ)
{
continue;
}
score++;
int index = e; // switch variables to keep e the same for the next loop around
do
{
intensities += eIntenisties[index];
index++;
} while (index < eLength && eMasses[index] < maxMZ);
}
}
return(score + intensities / tic);
}
private IEnumerable <QuantFile> LoadFiles(IEnumerable <string> filePaths, bool ms3Quant = false)
{
MSDataFile.CacheScans = false;
//int largestQuantPeak = 0;
int i = 0;
foreach (TagInformation tag in UsedTags.Values)
{
tag.UniqueTagNumber = i++;
tag.TotalSignal = 0;
tag.NormalizedTotalSignal = 0;
}
int largestQuantPeak = i - 1;
//int largestQuantPeak = UsedTags.Values.Select(tag => tag.UniqueTagNumber).Concat(new[] {0}).Max();
foreach (string filePath in filePaths)
{
Log("Processing file:\t" + filePath);
OnUpdateLog("Processing File " + filePath + "...");
QuantFile quantFile = new QuantFile(filePath);
StreamReader basestreamReader = new StreamReader(filePath);
int oldProgress = -1;
using (CsvReader reader = new CsvReader(basestreamReader, true))
{
while (reader.ReadNextRecord()) // go through csv and raw file to extract the info we want
{
int scanNumber = int.Parse(reader["Spectrum number"]);
string filenameID = reader["Filename/id"];
string rawFileName = filenameID.Split('.')[0];
bool isDecoy = reader["DEFLINE"].StartsWith("DECOY_");
ThermoRawFile rawFile;
if (!RawFiles.TryGetValue(rawFileName, out rawFile))
{
throw new ArgumentException("Cannot find this raw file: " + rawFileName + ".raw");
}
if (!rawFile.IsOpen)
{
rawFile.Open();
}
int progress = (int)(100 * (double)basestreamReader.BaseStream.Position / basestreamReader.BaseStream.Length);
if (progress != oldProgress)
{
OnProgressUpdate(progress);
oldProgress = progress;
}
//// Set default fragmentation to CAD / HCD
//FragmentationMethod ScanFragMethod = filenameID.Contains(".ETD.")
// ? FragmentationMethod.ETD
// : FragmentationMethod.CAD;
//if (ScanFragMethod == FragmentationMethod.ETD)
//{
// ScanFragMethod = FragmentationMethod.CAD;
// scanNumber += ETDQuantPosition;
//}
// Get the scan object for the sequence ms2 scan
MsnDataScan quantitationMsnScan = rawFile[scanNumber] as MsnDataScan;
double purity = 1;
if (CalculatePurity)
{
double mz = quantitationMsnScan.PrecursorMz;
int charge = quantitationMsnScan.PrecursorCharge;
DoubleRange isolationRange = MzRange.FromDa(mz, PurityWindowInTh);
MSDataScan parentScan = rawFile[quantitationMsnScan.ParentScanNumber];
purity = DeterminePurity(parentScan, mz, charge, isolationRange);
}
if (quantitationMsnScan == null)
{
OnUpdateLog("Spectrum Number " + scanNumber + " is not a valid MS2 scan from: " + rawFile.FilePath + ". Skipping PSM...");
continue;
}
if (MS3Quant)
{
quantitationMsnScan = null;
// Look forward to find associated MS3 quant scan (based on parent scan number)
int ms3ScanNumber = scanNumber + 1;
while (ms3ScanNumber < rawFile.LastSpectrumNumber)
{
if (rawFile.GetParentSpectrumNumber(ms3ScanNumber) == scanNumber)
{
quantitationMsnScan = rawFile[ms3ScanNumber] as MsnDataScan;
break;
}
ms3ScanNumber++;
}
if (quantitationMsnScan == null)
{
OnUpdateLog("Cannot find a MS3 spectrum associated with spectrum number " + scanNumber + ". Skipping PSM...");
continue;
}
}
Tolerance Tolerance = quantitationMsnScan.MzAnalyzer == MZAnalyzerType.IonTrap2D ? ItMassTolerance : FtMassTolerance;
bool isETD = quantitationMsnScan.DissociationType == DissociationType.ETD;
double injectionTime = quantitationMsnScan.InjectionTime;
//var massSpectrum = quantitationMsnScan.MassSpectrum;
var thermoSpectrum = rawFile.GetLabeledSpectrum(quantitationMsnScan.SpectrumNumber);
double noise = 0;
if (NoisebandCap)
{
// Noise is pretty constant over a small region, find the noise of the center of all isobaric tags
MassRange range = new MassRange(UsedTags.Keys[0], UsedTags.Keys[UsedTags.Count - 1]);
if (thermoSpectrum != null)
{
var peak = thermoSpectrum.GetClosestPeak(range.Mean, 500);
if (peak != null)
{
noise = peak.Noise;
}
else
{
OnUpdateLog("Spectrum (#" + quantitationMsnScan.SpectrumNumber + ") has no m/z peaks. Skipping PSM...");
continue;
}
}
else
{
OnUpdateLog("Spectrum (#" + quantitationMsnScan.SpectrumNumber + ") is low-resolution data without noise information. Skipping PSM...");
continue;
}
}
//Dictionary<TagInformation, QuantPeak> peaks = new Dictionary<TagInformation, QuantPeak>();
QuantPeak[] peaks = new QuantPeak[largestQuantPeak + 1];
// Read in the peak data
foreach (TagInformation tag in UsedTags.Values)
{
double tagMz = isETD
? tag.MassEtd
: tag.MassCAD;
var peak = thermoSpectrum.GetClosestPeak(Tolerance.GetRange(tagMz));
QuantPeak qPeak = new QuantPeak(tag, peak, injectionTime, quantitationMsnScan, noise, peak == null && NoisebandCap);
peaks[tag.UniqueTagNumber] = qPeak;
}
PurityCorrect(peaks, isDecoy);
PSM psm = new PSM(filenameID, scanNumber, peaks, purity);
quantFile.AddPSM(psm);
}
}
// Dispose of all raw files
foreach (ThermoRawFile rawFile in RawFiles.Values)
{
rawFile.Dispose();
}
OnUpdateLog("PSMs loaded " + quantFile.Psms.Count);
Log("PSMs Loaded:\t" + quantFile.Psms.Count);
yield return(quantFile);
}
}
