private List <Tuple <double, PointPairList> > GetMS3Spectra(int scan)
{
var result = new List <Tuple <double, PointPairList> >();
for (int i = scan + 1; i <= lastScan; i++)
{
var mslevel = reader.GetMsLevel(i);
if (mslevel != 3)
{
break;
}
var pplms3 = new PointPairList();
var ms3spectra = GetPeakList(i);
var ms3precursor = reader.GetPrecursorPeak(i);
foreach (var m in ms3spectra)
{
pplms3.Add(new PointPair(m.Mz, m.Intensity));
}
result.Add(new Tuple <double, PointPairList>(ms3precursor.Mz, pplms3));
}
result.Sort((m1, m2) => m1.Item1.CompareTo(m2.Item1));
return(result);
}
private List <SrmScan> GetMRMScans(string directory)
{
var fileName = GetPeakFileName(directory);
if (File.Exists(fileName))
{
SetProgressMessage("Reading scan from " + fileName + " ...");
return(new SrmScanFileFormat().ReadFromFile(fileName));
}
else
{
List <PeakList <Peak> > pkls = new List <PeakList <Peak> >();
SetProgressMessage("Reading scan from " + directory + " ...");
IRawFile reader = RawFileFactory.GetRawFileReader(directory);
try
{
var firstCount = reader.GetFirstSpectrumNumber();
var lastCount = reader.GetLastSpectrumNumber();
Progress.SetRange(firstCount, lastCount);
Progress.SetPosition(firstCount);
for (int i = firstCount; i <= lastCount; i++)
{
if (reader.GetMsLevel(i) != 2)
{
continue;
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.Increment(1);
var pkl = reader.GetPeakList(i);
var precursor = reader.GetPrecursorPeak(i);
if (precursor != null)
{
pkl.PrecursorMZ = precursor.Mz;
pkl.PrecursorCharge = precursor.Charge;
}
pkl.ScanTimes.Add(new ScanTime(i, reader.ScanToRetentionTime(i)));
pkls.Add(pkl);
}
List <SrmScan> result = new List <SrmScan>();
pkls.ForEach(m => m.ForEach(n => result.Add(new SrmScan(m.PrecursorMZ, n.Mz, m.ScanTimes[0].RetentionTime, n.Intensity, true))));
new SrmScanFileFormat().WriteToFile(fileName, result);
SetProgressMessage("finished.");
return(result);
}
finally
{
reader.Close();
}
}
}
public List <PrecursorItem> QueryPrecursorFromProductIon(QueryItem productIon, double ppmProductTolerance, double ppmPrecursorTolerance)
{
List <PrecursorItem> result = new List <PrecursorItem>();
int firstScan = reader.GetFirstSpectrumNumber();
int lastScan = reader.GetLastSpectrumNumber();
double mzTolerance = PrecursorUtils.ppm2mz(productIon.ProductIonMz, ppmProductTolerance);
PeakList <Peak> lastFullScan = new PeakList <Peak>();
Progress.SetRange(firstScan, lastScan);
for (int scan = firstScan; scan <= lastScan; scan++)
{
Progress.SetPosition(scan);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
//ignore ms 1
if (reader.GetMsLevel(scan) == 1)
{
lastFullScan = ReadScan(scan);
continue;
}
//read all peaks
PeakList <Peak> pkl = ReadScan(scan);
//find product ions
PeakList <Peak> productIons = pkl.FindPeak(productIon.ProductIonMz, mzTolerance);
if (productIons.Count == 0)
{
continue;
}
//get minimum product ion intensity
double maxIntensity = pkl.FindMaxIntensityPeak().Intensity;
double relativeIntensity = productIons.FindMaxIntensityPeak().Intensity / maxIntensity;
if (relativeIntensity < productIon.MinRelativeIntensity)
{
continue;
}
Peak peak = reader.GetPrecursorPeak(scan);
double precursorMzTolerance = PrecursorUtils.ppm2mz(peak.Mz, ppmPrecursorTolerance);
var precursorPkl = lastFullScan.FindPeak(peak.Mz, precursorMzTolerance);
bool isotopic = false;
if (precursorPkl.Count == 0)
{
isotopic = true;
precursorPkl = lastFullScan.FindPeak(peak.Mz - 1.0, precursorMzTolerance);
}
if (precursorPkl.Count == 0)
{
precursorPkl = lastFullScan.FindPeak(peak.Mz + 1.0, precursorMzTolerance);
}
var precursorInFullMs = precursorPkl.FindMaxIntensityPeak();
var precursor = new PrecursorItem()
{
Scan = scan,
ProductIonRelativeIntensity = relativeIntensity
};
if (isotopic && precursorInFullMs != null)
{
precursor.PrecursorMZ = precursorInFullMs.Mz;
precursor.IsIsotopic = true;
}
else
{
precursor.PrecursorMZ = peak.Mz;
precursor.IsIsotopic = false;
}
if (precursorInFullMs != null)
{
precursor.PrecursorIntensity = precursorInFullMs.Intensity;
}
result.Add(precursor);
}
var precursorMzs = from item in result
group item by item.PrecursorMZ into mzGroup
let mzcount = mzGroup.Where(m => m.PrecursorIntensity > 0).Count()
orderby mzcount descending
select mzGroup.Key;
foreach (var mz in precursorMzs)
{
double mzPrecursorTolerance = PrecursorUtils.ppm2mz(mz, ppmPrecursorTolerance);
foreach (var item in result)
{
if (!item.IsIsotopic)
{
continue;
}
if (Math.Abs(item.PrecursorMZ - mz) <= mzPrecursorTolerance)
{
item.PrecursorMZ = mz;
}
}
}
return(result);
}
