/// <summary>
/// Loads spectra from Raw files
/// </summary>
/// <returns></returns>
public Dictionary <Sample, Spectra> LoadSpectras(bool loadMS = true, bool filterMS2 = true)
{
//TODO test compatibility with QExactive, mzML ... other known formats
AllSpectras = new Dictionary <Sample, Spectra>();
for (int i = 0; i < Project.Count; i++)
{
Sample sample = Project[i];
string trackFile = vsCSV.GetFolder(sample.sSDF) + vsCSV.GetFileName_NoExtension(sample.sSDF) + "_Tracks.csv";
string msmsIonFile = vsCSV.GetFolder(sample.sSDF) + vsCSV.GetFileName_NoExtension(sample.sSDF) + "_MSMSIons.csv";
if (dbOptions.LoadSpectraIfFound && System.IO.File.Exists(trackFile) &&
System.IO.File.Exists(msmsIonFile))
{
dbOptions.ConSole.WriteLine("Loading Sectra from " + trackFile + " AND " + msmsIonFile);
if (loadMS)
{
AllSpectras.Add(sample, Spectra.Import(msmsIonFile, trackFile, dbOptions));
}
else
{
AllSpectras.Add(sample, Spectra.Import(msmsIonFile, null, dbOptions));
}
}
else
{
dbOptions.ConSole.WriteLine("Loading Sectra " + sample.sSDF);
pwiz.CLI.msdata.MSDataFile msFile = new pwiz.CLI.msdata.MSDataFile(sample.sSDF);
Spectra spectra = Spectra.Load(msFile, dbOptions, sample.sSDF, loadMS, filterMS2);
spectra.Sort(ProductSpectrum.AscendingPrecursorMassComparison);
dbOptions.ConSole.WriteLine(sample.sSDF + " [" + spectra.Count + " msms scans]");
if (dbOptions.SaveMS1Peaks)
{
spectra.ExportTracks(trackFile);
}
if (dbOptions.SaveMSMSPeaks)
{
spectra.ExportMSMS(msmsIonFile);
}
AllSpectras.Add(sample, spectra);
}
}
return(AllSpectras);
}
public static Spectra Import(string filenameMSMS, string filenameTracks, DBOptions dbOptions)
{
Spectra spectra = new Spectra();
vsCSV csv = new vsCSV(filenameMSMS);
if (csv.LINES_LIST.Count == 0 || csv.LINES_LIST[0].CompareTo(ProductSpectrum.TITLE) != 0)
{
return(null);
}
for (int i = 1; i < csv.LINES_LIST.Count; i++)
{
string[] splits = csv.LINES_LIST[i].Split(vsCSV._Generic_Separator);
double mz = double.Parse(splits[3]);
int charge = int.Parse(splits[5]);
int nbPeaks = int.Parse(splits[9]);
GraphML_List <MsMsPeak> peaks = new GraphML_List <MsMsPeak>(nbPeaks);
i++;
for (int j = 0; j < nbPeaks; i++, j++)
{
try
{
string[] splitPeaks = csv.LINES_LIST[i].Split('\t');
if (splitPeaks.Length > 2)
{
peaks.Add(new MsMsPeak(double.Parse(splitPeaks[0]), double.Parse(splitPeaks[1]), int.Parse(splitPeaks[2])));
}
else
{
peaks.Add(new MsMsPeak(double.Parse(splitPeaks[0]), double.Parse(splitPeaks[1]), 0));
}
}
catch (Exception)
{
dbOptions.ConSole.WriteLine("Error parsing line : " + csv.LINES_LIST[i]);
}
}
spectra.AddMSMS(new ProductSpectrum(int.Parse(splits[0]), double.Parse(splits[1]), splits[2], mz, double.Parse(splits[4]), charge, Proteomics.Utilities.Numerics.MassFromMZ(mz, charge), peaks, double.Parse(splits[8]), double.Parse(splits[10]), double.Parse(splits[11])));
}
if (!string.IsNullOrEmpty(filenameTracks))
{
spectra.tracks = Tracks.Import(filenameTracks, dbOptions);
}
return(spectra);
}
private static Tracks ComputeSpectraTracks(Spectra spectra, DBOptions options, string outputFilename, int missingScan, int centroid, int minPeaks, double valleyFactor, MaxQuant.CentroidPosition centroidMethod)
{
//Trail.RemoveFinished(ref trails, spectra, -1);
double[] centerMassArray;
float[] centerMassErrorArray;
float[] intensityArray;
float[] minTimeArray;
float[] maxTimeArray;
long[] filePosArray;
//TODO Cycle values to optimize missing scans and centroid values
string file = null;
if (options.WriteMaxQuantPeakFile)
{
file = options.OutputFolder + vsCSV.GetFileName_NoExtension(outputFilename) + "_Peaks.txt";
}
MaxQuant.PeakDetection.Detect(file,
missingScan, //*1-2-3-4-5
centroid, //*1-2-3-4-5-6-7-8-9-10
centroidMethod, //*
false, 0, options.precursorMassTolerance.Value, //TODO ensure its always in ppm
minPeaks, //*1-2-3-4-5-6-7-8-9-10
valleyFactor, //*0.1-0.2-0.3-...-3.0
true,
0,
new Trinity.MaxQuant.RawFileWrapper(spectra),
true,
null, out centerMassArray, out centerMassErrorArray, out intensityArray, out minTimeArray, out maxTimeArray, out filePosArray);
Tracks tracks = new Tracks();
for (int i = 0; i < centerMassArray.Length; i++)
{
tracks.AddTrack(centerMassArray[i], (minTimeArray[i] + maxTimeArray[i]) * 0.5, minTimeArray[i], maxTimeArray[i], intensityArray[i]);
}
return(tracks);
}
public void GenerateQueries(Sample entry, Spectra spectra, Tracks tracks)//, double mz, double rt, double intensity)
{
Dictionary <Track, Precursor> Tracks = new Dictionary <Track, Precursor>();
Dictionary <Track, Precursor> Isotopes = new Dictionary <Track, Precursor>();
//Create one query per Spectrum-Precursor duo, including Isotopes in the process to ease search
//For further analysis, maintain a list of precursors (excluding isotopes)
int nbMissedTrack = 0;
//vsSDF sdf = entry.GetSDF();// Samples.LoadSDF(entry);
//tracks.PrepareRtSort();
//sdf.TRACKS_LIST.PrepareRtSort();
spectra.Sort(ProductSpectrum.AscendingPrecursorMassComparison);
foreach (ProductSpectrum spectrum in spectra)
{
NbSpectrum++;
double intensityCumul = 0.0;
bool foundCharge = false;
Track closestTrack = null;
List <Query> newQueries = new List <Query>();
//TODO No threshold on sdf files, and preferably a C# routine that does what MassSense do
foreach (Track track in tracks.GetTracksInMzRange(spectrum.PrecursorMZ, spectrum.IsolationWindow * dbOptions.EffectiveIsolationWindowRatio))//TODO Optimize this value
{
Precursor prec = null;
if (track.RT_Min <= spectrum.RetentionTimeInMin &&
track.RT_Max >= spectrum.RetentionTimeInMin)
{
if (closestTrack == null || Math.Abs(track.MZ - spectrum.PrecursorMZ) < Math.Abs(closestTrack.MZ - spectrum.PrecursorMZ))
{
closestTrack = track;
}
if (Isotopes.ContainsKey(track))
{
break;
}
if (Tracks.ContainsKey(track))
{
prec = Tracks[track];
}
else
{
GraphML_List <Precursor> isotopes = GetIsotopes(track, dbOptions, tracks, entry);
if (isotopes.Count > 0)
{
prec = new Precursor(track, isotopes[0].Charge, entry, 0.0, isotopes);
Tracks.Add(track, prec);
prec.OtherCharges = GetOtherCharges(prec, dbOptions, tracks, entry);
foreach (Precursor isotope in prec.Isotopes)
{
if (!Isotopes.ContainsKey(isotope.Track))
{
Isotopes.Add(isotope.Track, isotope);
}
}
}
}
if (prec != null)
{
intensityCumul += track.INTENSITY;
newQueries.Add(new Query(dbOptions, entry, spectrum, prec, NbSpectrum));
if (prec.Charge == spectrum.PrecursorCharge)
{
foundCharge = true;
}
}
}
}
if (!foundCharge)
{
/*if (closestTrack != null && Tracks.ContainsKey(closestTrack) && Math.Abs(Numerics.CalculateMassError(closestTrack.MZ, spectrum.PrecursorMZ, dbOptions.precursorMassTolerance.Units)) < dbOptions.precursorMassTolerance.Value)
* {
* if(closestTrack.RT_Min > (float)(spectrum.RetentionTimeInMin - dbOptions.ComputedRetentionTimeDiff))
* closestTrack.RT_Min = (float)(spectrum.RetentionTimeInMin - dbOptions.ComputedRetentionTimeDiff);
* if (closestTrack.RT_Max < (float)(spectrum.RetentionTimeInMin + dbOptions.ComputedRetentionTimeDiff))
* closestTrack.RT_Max = (float)(spectrum.RetentionTimeInMin + dbOptions.ComputedRetentionTimeDiff);
* if (closestTrack.INTENSITY < spectrum.PrecursorIntensity)
* closestTrack.INTENSITY = spectrum.PrecursorIntensity;
*
* Precursor prec = Tracks[closestTrack];
* if (prec.Charge == spectrum.PrecursorCharge)
* {
* Add(new Query(dbOptions, entry, spectrum, prec, NbSpectrum));
* }
* else
* {
* Precursor newPrec = new Precursor(closestTrack, spectrum.PrecursorCharge, entry);
* Add(new Query(dbOptions, entry, spectrum, newPrec, NbSpectrum));
* }
* }
* else//*/
{
nbMissedTrack++;
closestTrack = new Track((float)spectrum.PrecursorMZ, (float)spectrum.RetentionTimeInMin, spectrum.PrecursorIntensity,
(float)(spectrum.RetentionTimeInMin - dbOptions.ComputedRetentionTimeDiff), (float)(spectrum.RetentionTimeInMin + dbOptions.ComputedRetentionTimeDiff),
true);
Precursor prec = new Precursor(closestTrack, spectrum.PrecursorCharge, entry);
Tracks.Add(closestTrack, prec);
Add(new Query(dbOptions, entry, spectrum, prec, NbSpectrum));
}
}//*/
if (newQueries.Count > 0)
{
//Remove precursors if estimated fragment intensities are too low (based on precursor intensity ratios and isolation window placement)
foreach (Query q in newQueries)
{
//if (q.precursor.Track.INTENSITY > intensityCumul * dbOptions.MinimumPrecursorIntensityRatioInIsolationWindow)//Need to be 5% of all intensity
//{
this.Add(q);
//}
}
}
Console.Write("\r{0}% ", ((100 * NbSpectrum) / spectra.Count));
}
Console.Write("\r{0}% ", 100);
//Sort queries to ease search
this.Sort(AscendingPrecursorMassComparison);
foreach (Track track in Tracks.Keys)
{
if (!Isotopes.ContainsKey(track))
{
Precursors.Add(Tracks[track]);
}
}
//TODO Validate this approach
//REMOVE QUERIES RELATED TO AN ISOTOPE and Compute the average CoElution
Dictionary <ProductSpectrum, double> DicOfSpectrumIntensities = new Dictionary <ProductSpectrum, double>();
for (int i = 0; i < this.Count;)
{
Query query = this[i];
if (!Isotopes.ContainsKey(query.precursor.Track))
{
if (!DicOfSpectrumIntensities.ContainsKey(query.spectrum))
{
DicOfSpectrumIntensities.Add(query.spectrum, query.precursor.Track.INTENSITY);
}
else
{
DicOfSpectrumIntensities[query.spectrum] += query.precursor.Track.INTENSITY;
}
i++;
}
else
{
this.RemoveAt(i);
}
}
//REMOVE Queries with Precursor intensities too low
for (int i = 0; i < this.Count;)
{
Query query = this[i];
if (query.precursor.Track.INTENSITY < DicOfSpectrumIntensities[query.spectrum] * dbOptions.MinimumPrecursorIntensityRatioInIsolationWindow)
{
this.RemoveAt(i);
}
else
{
i++;
}
}//*/
Dictionary <ProductSpectrum, int> DicOfSpectrumTracks = new Dictionary <ProductSpectrum, int>();
for (int i = 0; i < this.Count;)
{
Query query = this[i];
if (!Isotopes.ContainsKey(query.precursor.Track))
{
if (!DicOfSpectrumTracks.ContainsKey(query.spectrum))
{
DicOfSpectrumTracks.Add(query.spectrum, 1);
}
else
{
DicOfSpectrumTracks[query.spectrum]++;
}
i++;
}
else
{
this.RemoveAt(i);
}
}
double averageNbPrecursorPerSpectrum = 0;
int nbSpectrumMatchedToTrack = 0;
foreach (ProductSpectrum spectrum in DicOfSpectrumTracks.Keys)
{
nbSpectrumMatchedToTrack++;
averageNbPrecursorPerSpectrum += DicOfSpectrumTracks[spectrum];
}
dbOptions.ConSole.WriteLine(entry.sSDF + " :" + Precursors.Count + " precursors [" + Isotopes.Count + " isotopes] spreaded in " + Count + " queries [" + nbMissedTrack + " trackless precursors]");
dbOptions.ConSole.WriteLine("Average Precursors per Spectrum : " + averageNbPrecursorPerSpectrum / (double)nbSpectrumMatchedToTrack);
}
public static Spectra Load(pwiz.CLI.msdata.MSDataFile msFile, DBOptions options, string filePath, bool loadMS = true, bool filterMS2 = true)
{
//Find file name in msFile;
string mzMlFilepath = filePath;
int num_spectra = msFile.run.spectrumList.size();
Spectra spectra = new Spectra(num_spectra);
//List<Trail> trails = new List<Trail>();
MS1Spectrum previousMS1 = null;
try
{
//TODO DONT forget to remove the limiter
//int maxNbMSMS = 10;
double LastMs1InjectionTime = 0;
for (int i = 0; i < num_spectra /* && i < 200*/; i++)//TODO Fix that later!
{
//Spectrum
pwiz.CLI.msdata.Spectrum spec = msFile.run.spectrumList.spectrum(i, true);
if (spec.precursors.Count > 0 || spec.cvParam(pwiz.CLI.cv.CVID.MS_ms_level).value > 1)//is an MSMS
{
double retention_time = spec.scanList.scans[0].cvParam(pwiz.CLI.cv.CVID.MS_scan_start_time).timeInSeconds() / 60.0;
//List precursors and their intensities
double precursor_mz = 0;//Is there a value for the time a scan took to complete?
int charge = 2;
double precursor_intensity = 0;
string fragmentation_method = "unknown";
double isolationWindow = 1.0;
double injectionTime = spec.scanList.scans[0].cvParam(pwiz.CLI.cv.CVID.MS_ion_injection_time).value;
foreach (pwiz.CLI.msdata.Precursor precursor in spec.precursors)
{
fragmentation_method = precursor.activation.cvParams[0].name;
if (precursor.isolationWindow.cvParams.Count > 2 && (double)precursor.isolationWindow.cvParams[1].value == (double)precursor.isolationWindow.cvParams[2].value)
{
isolationWindow = precursor.isolationWindow.cvParams[1].value;
}
else if (precursor.isolationWindow.cvParams.Count > 2)
{
options.ConSole.WriteLine("Weird Isolation Window");
}
foreach (pwiz.CLI.msdata.SelectedIon ion in precursor.selectedIons)
{
//Cycle through MS to get real precursor intensities
precursor_mz = ion.cvParams[0].value;
if (ion.cvParams.Count > 1)
{
charge = (int)ion.cvParams[1].value;
}
//else
// dbOptions.ConSole.WriteLine("No charge computed for precursor ");
if (ion.cvParams.Count > 2)
{
precursor_intensity = ion.cvParams[2].value;
}
}
}
int scan_index = i;
int scan_number = scan_index + 1;
pwiz.CLI.msdata.BinaryDataArray mz = spec.getMZArray();
pwiz.CLI.msdata.BinaryDataArray intensity = spec.getIntensityArray();
int num_peaks = mz.data.Count;
if (num_peaks != intensity.data.Count)
{
options.ConSole.WriteLine("PreoteWizard reports peaks arrays (mz/intensity) of different sizes : (" + num_peaks + "/" + intensity.data.Count + ")");
if (intensity.data.Count < num_peaks)
{
num_peaks = intensity.data.Count;
}
}
GraphML_List <MsMsPeak> peaks = new GraphML_List <MsMsPeak>(num_peaks);
for (int k = 0; k < num_peaks; k++)
{
if (intensity.data[k] > 0)
{
MsMsPeak peak = new MsMsPeak(mz.data[k], intensity.data[k], 0);
peaks.Add(peak);
}
}
mz.Dispose(); mz = null;
intensity.Dispose(); intensity = null;
peaks.Sort(MsMsPeak.AscendingMzComparison);
if (filterMS2)
{
//peaks = AssignChargeStates(peaks, options.maximumAssumedPrecursorChargeState, options.precursorMassTolerance);
//peaks = Deisotopebkp(peaks, options.maximumAssumedPrecursorChargeState, options.precursorMassTolerance);
peaks = AssignChargeStatesAndDeisotope(peaks, options.MaximumPrecursorChargeState, new MassTolerance(options.productMassTolerance.Value * 0.5, options.productMassTolerance.Units));
peaks = FilterPeaks(peaks, options.MaximumNumberOfFragmentsPerSpectrum);
//TODO Add Contaminant removal
//peaks = ContaminantMasses.RemoveContaminantsFromMzSortedList(peaks, options.productMassTolerance);
//Can sometime be sorted by intensity after this call
//peaks = FilterPeaksV2(peaks);
peaks.Sort(MsMsPeak.AscendingMzComparison);
}
/*//TODO Validate that in most cases, next steps can calculate missing charge
* if (charge == 0)
* {
* for (int c = options.minimumAssumedPrecursorChargeState; c <= options.maximumAssumedPrecursorChargeState; c++)
* {
* if (options.assignChargeStates)
* {
* peaks = AssignChargeStates(peaks, c, options.productMassTolerance);
* if (options.deisotope)
* {
* peaks = Deisotope(peaks, c, options.productMassTolerance);
* }
* }
*
* double precursor_mass = Utilities.MassFromMZ(precursor_mz, c);
*
* ProductSpectrum spectrum = new ProductSpectrum(mzMlFilepath, scan_number, retention_time, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
* spectra.Add(spectrum);
* }
* }
* else//*/
{/*
* if (options.assignChargeStates)
* {
* peaks = AssignChargeStatesbkp(peaks, charge, options.productMassTolerance);
* if (options.deisotope)
* {
* peaks = Deisotopebkp(peaks, charge, options.productMassTolerance);
* }
* }//*/
//peaks = AssignChargeStatesAndDeisotope(peaks, options.maximumAssumedPrecursorChargeState, options.productMassTolerance);
double precursor_mass = Numerics.MassFromMZ(precursor_mz, charge);
ProductSpectrum spectrum = new ProductSpectrum(scan_number, retention_time, fragmentation_method, precursor_mz, precursor_intensity, charge, precursor_mass, peaks, isolationWindow, injectionTime, LastMs1InjectionTime);
spectra.AddMSMS(spectrum);
//zones.Add(new Zone(precursor_mz - isolationWindow, precursor_mz + isolationWindow, retention_time));
}
//if (spectra.Count >= maxNbMSMS)
// i = 10000000;
}
else //Is an MS
{
LastMs1InjectionTime = spec.scanList.scans[0].cvParam(pwiz.CLI.cv.CVID.MS_ion_injection_time).value;
if (loadMS)
{
double retention_time = spec.scanList.scans[0].cvParam(pwiz.CLI.cv.CVID.MS_scan_start_time).timeInSeconds() / 60.0;
pwiz.CLI.msdata.BinaryDataArray mz = spec.getMZArray();
pwiz.CLI.msdata.BinaryDataArray intensity = spec.getIntensityArray();
if (previousMS1 != null)
{
previousMS1.ScanDuration = retention_time - previousMS1.RetentionTimeInMin;
spectra.MS1s.Add(previousMS1);
}
previousMS1 = new MS1Spectrum(i, retention_time, intensity.data, mz.data, 1);
//Trail.Follow(mz.data, intensity.data, retention_time, ref trails, options);
//Trail.RemoveFinished(ref trails, spectra, 1);
}
}
spec.Dispose(); spec = null;
Console.Write("\r{0}% ", ((100 * i) / num_spectra));
}
if (previousMS1 != null)
{
spectra.MS1s.Add(previousMS1);
}
/*
* //Optimization of Track following parameters
* long nbChargedTracks = 0;
* for(int missingScans = 1; missingScans < 5; missingScans++)
* {
* for(int centroid = 1; centroid < 5; centroid++)
* {
* for(int minPeaks = 1; minPeaks < 7; minPeaks++)
* {
* for(double valleyFactor = 0.1; valleyFactor < 4; valleyFactor += 0.3)
* {
* //weightedMean
* Tracks tracks = ComputeSpectraTracks(spectra, options, mzMlFilepath, missingScans, centroid, minPeaks, valleyFactor, MaxQuant.CentroidPosition.weightedMean);
* tracks.Sort(Tracks.AscendingPrecursorMassComparison);
* long cumulIsotopes = 0;
* foreach (stTrack track in tracks)
* cumulIsotopes += Queries.GetIsotopes(track, options, tracks, sample).Count;
* if (cumulIsotopes > nbChargedTracks)
* {
* nbChargedTracks = cumulIsotopes;
* dbOptions.ConSole.WriteLine(missingScans + "," + centroid + "," + minPeaks + "," + valleyFactor + ",weightedMean");
* }
*
* //Gaussian
* tracks = ComputeSpectraTracks(spectra, options, mzMlFilepath, missingScans, centroid, minPeaks, valleyFactor, MaxQuant.CentroidPosition.gaussian);
* tracks.Sort(Tracks.AscendingPrecursorMassComparison);
* cumulIsotopes = 0;
* foreach (stTrack track in tracks)
* cumulIsotopes += Queries.GetIsotopes(track, options, tracks, sample).Count;
* if (cumulIsotopes > nbChargedTracks)
* {
* nbChargedTracks = cumulIsotopes;
* dbOptions.ConSole.WriteLine(missingScans + "," + centroid + "," + minPeaks + "," + valleyFactor + ",Gaussian");
* }
* }
* }
* }
* }//*/
if (spectra.MS1s.Count > 0)
{
spectra.tracks = ComputeSpectraTracks(spectra, options, mzMlFilepath, 3, 1, 3, 1.7, MaxQuant.CentroidPosition.weightedMean);
}
else
{
spectra.tracks = new Tracks();
}
spectra.tracks.Sort(Tracks.AscendingPrecursorMassComparison);
Console.Write("\r{0}% ", 100);
//ContaminantMasses.DisplayContaminants();
}
catch (Exception ex)
{
options.ConSole.WriteLine(ex.StackTrace);
options.ConSole.WriteLine(ex.Message);
}
return(spectra);
}
