public void ParallelRun(string path, string outputDir, AveragineType type, ChargerType charger)
{
string file = Path.GetFileNameWithoutExtension(path) + ".mzML";
string output = Path.Combine(outputDir, file);
MZMLProducer mZMLProducer = new MZMLProducer();
var model = mZMLProducer.Produce(path, progressingCounter.Add, type, (mzMLWriter.ChargerType)charger);
var serializer = new XmlSerializer(model.GetType());
var encoding = Encoding.GetEncoding("ISO-8859-1");
XmlWriterSettings xmlWriterSettings = new XmlWriterSettings
{
Indent = true,
OmitXmlDeclaration = false,
Encoding = Encoding.UTF8
};
using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
using (XmlWriter xmlWriter = XmlWriter.Create(writer, xmlWriterSettings))
{
serializer.Serialize(xmlWriter, model);
}
}
}
// update progress
progress.Add();
}
private void SelectTypes(object sender, RoutedEventArgs e)
{
if (Peptides.IsChecked == true)
{
type = AveragineType.Peptide;
}
else if (Glycopeptides.IsChecked == true)
{
type = AveragineType.GlycoPeptide;
}
else if (Glycan.IsChecked == true)
{
type = AveragineType.Glycan;
}
else if (PermethylatedGlycan.IsChecked == true)
{
type = AveragineType.PermethylatedGlycan;
}
}
public Dictionary <Element, double> Composition(AveragineType type)
{
switch (type)
{
case AveragineType.Peptide:
return(Peptide);
case AveragineType.GlycoPeptide:
return(Glycopeptide);
case AveragineType.Glycan:
return(Glycan);
case AveragineType.PermethylatedGlycan:
return(PermethylatedGlycan);
default:
break;
}
return(Peptide);
}
public Averagine(AveragineType type = AveragineType.GlycoPeptide)
{
Type = type;
}
public void ParallelRun(string path, string outputDir, AveragineType type, ChargerType chargerType)
{
string file = Path.GetFileNameWithoutExtension(path) + ".mgf";
string output = Path.Combine(outputDir, file);
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking(ms1PrcisionPPM);
reader.Init(path);
Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >();
int current = -1;
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
for (int i = start; i < end; i++)
{
if (reader.GetMSnOrder(i) == 1)
{
current = i;
scanGroup[i] = new List <int>();
}
else if (reader.GetMSnOrder(i) == 2)
{
scanGroup[current].Add(i);
}
}
List <MS2Info> ms2Infos = new List <MS2Info>();
Parallel.ForEach(scanGroup, (scanPair) =>
{
if (scanPair.Value.Count > 0)
{
ISpectrum ms1 = reader.GetSpectrum(scanPair.Key);
foreach (int i in scanPair.Value)
{
double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i));
List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange);
if (ms1Peaks.Count() == 0)
{
continue;
}
// insert pseudo peaks for large gap
List <IPeak> peaks = new List <IPeak>();
double precision = 0.02;
double last = ms1Peaks.First().GetMZ();
foreach (IPeak peak in ms1Peaks)
{
if (peak.GetMZ() - last > precision)
{
peaks.Add(new GeneralPeak(last + precision / 2, 0));
peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0));
}
peaks.Add(peak);
last = peak.GetMZ();
}
List <IPeak> majorPeaks = picking.Process(peaks);
ICharger charger = new Patterson();
if (chargerType == ChargerType.Fourier)
{
charger = new Fourier();
}
else if (chargerType == ChargerType.Combined)
{
charger = new PattersonFourierCombine();
}
int charge = charger.Charge(peaks, mz - searchRange, mz + searchRange);
// find evelope cluster
EnvelopeProcess envelope = new EnvelopeProcess();
var cluster = envelope.Cluster(majorPeaks, mz, charge);
if (cluster.Count == 0)
{
continue;
}
// find monopeak
Averagine averagine = new Averagine(type);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
double precursorMZ = result.GetMZ();
// write mgf
ISpectrum ms2 = reader.GetSpectrum(i);
IProcess processer = new WeightedAveraging(new LocalNeighborPicking());
ms2 = processer.Process(ms2);
MS2Info ms2Info = new MS2Info
{
PrecursorMZ = result.GetMZ(),
PrecursorCharge = charge,
Scan = ms2.GetScanNum(),
Retention = ms2.GetRetention(),
Peaks = ms2.GetPeaks()
};
lock (resultLock)
{
ms2Infos.Add(ms2Info);
}
}
}
readingProgress.Add(scanGroup.Count);
});
ms2Infos = ms2Infos.OrderBy(m => m.Scan).ToList();
using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
foreach (MS2Info ms2 in ms2Infos)
{
WriteMGF(writer, path + ",SCANS=" + ms2.Scan.ToString() + ",PRECURSOR=" + ms2.PrecursorMZ, ms2.PrecursorMZ, ms2.PrecursorCharge,
ms2.Scan, ms2.Retention * 60, reader.GetActivation(ms2.Scan), ms2.Peaks);
writer.Flush();
}
}
}
// update progress
progress.Add();
}
public Run Read(string path, AveragineType type, ChargerType charger, string defaultDataProcessingRef,
ProgressUpdate updater)
{
Run data = new Run();
// init reader
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking(ms1PrcisionPPM);
IProcess process = new WeightedAveraging(new LocalNeighborPicking());
reader.Init(path);
data.spectrumList = new SpectrumList();
Dictionary <int, Spectrum> spectrumMap = new Dictionary <int, Spectrum>();
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >();
int current = -1;
for (int i = start; i < end; i++)
{
if (reader.GetMSnOrder(i) == 1)
{
current = i;
scanGroup[i] = new List <int>();
}
else if (reader.GetMSnOrder(i) == 2)
{
scanGroup[current].Add(i);
}
}
Parallel.ForEach(scanGroup, (scanPair) => {
if (scanPair.Value.Count > 0)
{
int parentScan = scanPair.Key;
ISpectrum ms1 = null;
List <IPeak> majorPeaks = new List <IPeak>();
Spectrum ms1Spectrum =
ThermoRawRunFactoryHelper.GetMS1Spectrum(ref reader, parentScan, ref ms1);
if (ms1Spectrum != null)
{
lock (resultLock)
{
spectrumMap[parentScan] = ms1Spectrum;
}
}
foreach (int scan in scanPair.Value)
{
Spectrum ms2Spectrum =
ThermoRawRunFactoryHelper.GetMS2Spectrum(ref reader, scan, type, charger, picking, process, ms1);
if (ms2Spectrum != null)
{
lock (resultLock)
{
spectrumMap[scan] = ms2Spectrum;
}
}
}
}
updater(scanGroup.Count);
});
List <Spectrum> spectrumList =
spectrumMap.OrderBy(s => s.Key).Select(s => s.Value).ToList();
data.spectrumList.spectrum = new Spectrum[spectrumList.Count];
spectrumList = spectrumList.OrderBy(x => int.Parse(x.id.Substring(5))).ToList();
for (int i = 0; i < spectrumList.Count; i++)
{
int scan = int.Parse(spectrumList[i].id.Substring(5));
data.spectrumList.spectrum[i] = spectrumList[i];
data.spectrumList.spectrum[i].index = (scan - 1).ToString();
data.spectrumList.spectrum[i].defaultArrayLength = spectrumList[i].defaultArrayLength;
}
data.spectrumList.count = spectrumList.Count.ToString();
data.spectrumList.defaultDataProcessingRef = defaultDataProcessingRef;
return(data);
}
public MSmzML Produce(string path, ProgressUpdate updater, AveragineType type, ChargerType charger)
{
var model = new MSmzML();
// cvList
model.cvList = new CVList();
CV[] cvArray = new CV[2];
cvArray[0] = new CV()
{
id = "MS",
fullName = "Proteomics Standards Initiative Mass Spectrometry Ontology",
version = "2.26.0",
URI = "http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
};
cvArray[1] = new CV
{
id = "UO",
fullName = "Unit Ontology",
version = "14:07:2009",
URI = "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"
};
model.cvList.cv = cvArray;
model.cvList.count = "2";
// fileDescription
model.fileDescription = new FileDescription();
model.fileDescription.fileContent = new FileContent();
model.fileDescription.fileContent.cvParam = new CVParam[2];
model.fileDescription.fileContent.cvParam[0] = new CVParam
{
cvRef = "MS",
accession = "MS:1000580",
name = "MSn spectrum",
value = ""
};
model.fileDescription.fileContent.cvParam[1] = new CVParam
{
cvRef = "MS",
accession = "MS:1000127",
name = "centroid spectrum",
value = ""
};
model.fileDescription.sourceFileList = new SourceFileList();
model.fileDescription.sourceFileList.sourceFile = new SourceFile[1];
string fileName = Path.GetFileName(path);
model.fileDescription.sourceFileList.sourceFile[0] = new SourceFile
{
id = fileName,
name = fileName,
location = path
};
model.fileDescription.sourceFileList.count = "1";
model.fileDescription.contact = new Contact();
model.fileDescription.contact.cvParam = new CVParam[2];
model.fileDescription.contact.cvParam[0] = new CVParam
{
cvRef = "MS",
accession = "MS:1000586",
name = "contact name",
value = contactPerson
};
model.fileDescription.contact.cvParam[1] = new CVParam
{
cvRef = "MS",
accession = "MS:1000589",
name = "contact email",
value = contactEmail
};
// softwareList
model.softwareList = new SoftwareList();
model.softwareList.software = new Software[1];
model.softwareList.software[0] = new Software
{
id = software,
version = softwareVersion
};
model.softwareList.count = "1";
// instrumentConfiguration
string instrumentConfigurationID = "UNKNOWN";
model.instrumentConfigurationList = new InstrumentConfigurationList();
model.instrumentConfigurationList.instrumentConfiguration = new InstrumentConfiguration[1];
model.instrumentConfigurationList.instrumentConfiguration[0] = new InstrumentConfiguration()
{
id = instrumentConfigurationID
};
model.instrumentConfigurationList.count = "1";
// data processing
model.dataProcessingList = new DataProcessingList();
model.dataProcessingList.dataProcessing = new DataProcessing[1];
model.dataProcessingList.dataProcessing[0] = new DataProcessing();
model.dataProcessingList.dataProcessing[0].id = dataProcessingID;
model.dataProcessingList.dataProcessing[0].processingMethod = new ProcessingMethod[1];
model.dataProcessingList.dataProcessing[0].processingMethod[0] = new ProcessingMethod()
{
order = "1",
softwareRef = software
};
model.dataProcessingList.dataProcessing[0].processingMethod[0].cvParam = new CVParam[2];
model.dataProcessingList.dataProcessing[0].processingMethod[0].cvParam[0] = new CVParam()
{
cvRef = "MS",
accession = "MS:1000035",
name = "peak picking",
value = ""
};
model.dataProcessingList.dataProcessing[0].processingMethod[0].cvParam[1] = new CVParam()
{
cvRef = "MS",
accession = "MS:1000544",
name = "Conversion to mzML",
value = ""
};
model.dataProcessingList.count = "1";
// spectrum data
ThermoRawRunFactory factory = new ThermoRawRunFactory();
model.run = factory.Read(path, type, charger,
model.dataProcessingList.dataProcessing[0].id, updater);
model.run.id = Guid.NewGuid().ToString();
model.run.defaultInstrumentConfigurationRef = instrumentConfigurationID;
return(model);
}
public static Spectrum GetMS2Spectrum(ref ThermoRawSpectrumReader reader,
int scan, AveragineType type, ChargerType chargerType, LocalMaximaPicking picking, IProcess process,
ISpectrum ms1)
{
// scan header
Spectrum spectrum = new Spectrum
{
id = "scan=" + scan.ToString()
};
double dLowMass = 0;
double dHighMass = 0;
double dTIC = 0;
double dBasePeakMass = 0;
double dBasePeakIntensity = 0;
reader.GetScanHeaderInfoForScanNum(scan, ref dLowMass, ref dHighMass,
ref dTIC, ref dBasePeakMass, ref dBasePeakIntensity);
SetScanHeader(spectrum, dLowMass, dHighMass, dTIC,
dBasePeakMass, dBasePeakIntensity);
// binary data
spectrum.binaryDataArrayList = new BinaryDataArrayList();
SetBinaryDataArrayHeader(spectrum.binaryDataArrayList);
spectrum.cvParam[0] = new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000511",
name = "ms level",
value = "2",
};
double mz = reader.GetPrecursorMass(scan, reader.GetMSnOrder(scan));
List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange);
if (ms1Peaks.Count() == 0)
{
return(null);
}
// insert pseudo peaks for large gaps
List <IPeak> peaks = new List <IPeak>();
double precision = 0.02;
double last = ms1Peaks.First().GetMZ();
foreach (IPeak peak in ms1Peaks)
{
if (peak.GetMZ() - last > precision)
{
peaks.Add(new GeneralPeak(last + precision / 2, 0));
peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0));
}
peaks.Add(peak);
last = peak.GetMZ();
}
List <IPeak> majorPeaks = picking.Process(peaks);
ICharger charger = new Patterson();
if (chargerType == ChargerType.Fourier)
{
charger = new Fourier();
}
else if (chargerType == ChargerType.Combined)
{
charger = new PattersonFourierCombine();
}
int charge = charger.Charge(peaks, mz - searchRange, mz + searchRange);
// find evelope cluster
EnvelopeProcess envelope = new EnvelopeProcess();
var cluster = envelope.Cluster(majorPeaks, mz, charge);
if (cluster.Count == 0)
{
return(null);
}
// find monopeak
Averagine averagine = new Averagine(type);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
// process spectrum
ISpectrum ms2 = reader.GetSpectrum(scan);
List <IPeak> ms2Peaks = process.Process(ms2).GetPeaks();
spectrum.binaryDataArrayList.binaryDataArray[0].binary =
ms2Peaks.SelectMany(p => BitConverter.GetBytes(p.GetMZ())).ToArray();
spectrum.binaryDataArrayList.binaryDataArray[1].binary =
ms2Peaks.SelectMany(p => BitConverter.GetBytes(p.GetIntensity())).ToArray();
spectrum.defaultArrayLength = ms2Peaks.Count.ToString();
spectrum.precursorList = new PrecursorList
{
count = "1",
precursor = new Precursor[1]
};
for (int i = 0; i < spectrum.precursorList.precursor.Length; i++)
{
spectrum.precursorList.precursor[i] = new Precursor();
}
spectrum.precursorList.precursor[0].selectedIonList = new SelectedIonList
{
count = "1",
selectedIon = new SelectedIon[1]
};
for (int i = 0; i < spectrum.precursorList.precursor[0].selectedIonList.selectedIon.Length; i++)
{
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[i] = new SelectedIon();
}
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam = new Component.CVParam[2];
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[0] = new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000744",
name = "selected ion m/z",
value = result.GetMZ().ToString(),
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z"
};
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[1] = new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000041",
name = "charge state",
value = charge.ToString()
};
spectrum.precursorList.precursor[0].activation = new Activation
{
cvParam = new Component.CVParam[1]
};
spectrum.precursorList.precursor[0].activation.cvParam[0] =
ActivationCVParam(reader.GetActivation(scan));
spectrum.binaryDataArrayList.binaryDataArray[0].encodedLength =
Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[0].binary).Length.ToString();
spectrum.binaryDataArrayList.binaryDataArray[1].encodedLength =
Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[1].binary).Length.ToString();
return(spectrum);
}
