private bool AcceptScan(SilacPeakListPair pair, SilacCompoundInfo sci, int lightMaxIndex, double lightMinPPM, double lightMaxPPM, int heavyMaxIndex, double heavyMinPPM, double heavyMaxPPM)
{
//如果轻重标中任意一个最高峰不存在，循环结束。
if (pair.Light[lightMaxIndex].Intensity == 0 || pair.Heavy[heavyMaxIndex].Intensity == 0)
{
return(false);
}
//轻标最高峰的ppm
double lightPPM = PrecursorUtils.mz2ppm(pair.Light[lightMaxIndex].Mz, sci.Light.Profile[lightMaxIndex].Mz - pair.Light[lightMaxIndex].Mz);
if (lightPPM < lightMinPPM || lightPPM > lightMaxPPM)
{
return(false);
}
//重标最高峰的ppm
double heavyPPM = PrecursorUtils.mz2ppm(pair.Heavy[heavyMaxIndex].Mz, sci.Heavy.Profile[heavyMaxIndex].Mz - pair.Heavy[heavyMaxIndex].Mz);
if (heavyPPM < heavyMinPPM || heavyPPM > heavyMaxPPM)
{
return(false);
}
return(true);
}
public void Quantify(string rawFileName, List <IIdentifiedSpectrum> spectra, string detailDir)
{
if (!Directory.Exists(detailDir))
{
Directory.CreateDirectory(detailDir);
}
var experimental = RawFileFactory.GetExperimental(rawFileName);
Dictionary <string, DifferentRetentionTimeEnvelopes> spectrumKeyMap = new Dictionary <string, DifferentRetentionTimeEnvelopes>();
Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> > envelopeSpectrumGroup = new Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> >();
double precursorPPM = GetPrecursorPPM(spectra);
try
{
_rawReader.Open(rawFileName);
int firstScanNumber = _rawReader.GetFirstSpectrumNumber();
int lastScanNumber = _rawReader.GetLastSpectrumNumber();
Progress.SetRange(1, spectra.Count);
int pepCount = 0;
for (int s = 0; s < spectra.Count; s++)
{
Console.WriteLine(s);
IIdentifiedSpectrum spectrum = spectra[s];
SilacQuantificationSummaryItem.ClearAnnotation(spectrum);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
int startScan = spectrum.Query.FileScan.FirstScan;
if (startScan > lastScanNumber)
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "OUT_OF_RANGE";
continue;
}
Progress.SetPosition(pepCount++);
IIdentifiedPeptide sp = spectrum.Peptide;
string seq = GetMatchSequence(spectrum);
IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(seq, spectrum.TheoreticalMH, spectrum.Query.Charge);
SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo);
//如果轻重离子理论质荷比一样，忽略
if (!sci.IsSilacData())
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "NOT_SILAC";
continue;
}
//如果轻重离子理论质荷比与观测值不一致，忽略
if (!sci.IsMzEquals(spectrum.ObservedMz, MAX_DELTA_MZ))
{
ValidateModifications(seq);
spectrum.GetOrCreateQuantificationItem().RatioStr = "WRONG_IDENTIFICATION";
continue;
}
//如果没有找到相应的FullScan，忽略
int identifiedFullScan = _rawReader.FindPreviousFullScan(startScan, firstScanNumber);
if (-1 == identifiedFullScan)
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE";
continue;
}
DifferentRetentionTimeEnvelopes pkls = FindEnvelopes(spectrumKeyMap, spectrum, sci);
SilacEnvelopes envelope = pkls.FindSilacEnvelope(identifiedFullScan);
//如果该scan被包含在已经被定量的结果中，忽略
if (envelope != null)
{
envelope.SetScanIdentified(identifiedFullScan, spectrum.IsExtendedIdentification());
envelopeSpectrumGroup[envelope].Add(spectrum);
continue;
}
//从原始文件中找出该spectrum的定量信息
int maxIndex = Math.Min(option.ProfileLength - 1, pkls.LightProfile.FindMaxIndex());
double mzTolerance = PrecursorUtils.ppm2mz(sci.Light.Mz, option.PPMTolerance);
//如果FullScan没有相应的离子，忽略。（鉴定错误或者扩展定量时候，会出现找不到pair的现象）
SilacPeakListPair splp = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, identifiedFullScan);
if (null == splp)
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE";
continue;
}
splp.IsIdentified = true;
splp.IsExtendedIdentification = spectrum.IsExtendedIdentification();
SilacEnvelopes envelopes = new SilacEnvelopes();
envelopes.Add(splp);
//向前查找定量信息
int fullScan = identifiedFullScan;
int scanNumber = 0;
while ((fullScan = _rawReader.FindPreviousFullScan(fullScan - 1, firstScanNumber)) != -1)
{
if (_rawReader.IsBadDataScan(fullScan))
{
continue;
}
scanNumber++;
var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber);
if (null == item)
{
break;
}
envelopes.Add(item);
}
envelopes.Reverse();
//向后查找定量信息
fullScan = identifiedFullScan;
scanNumber = 0;
while ((fullScan = _rawReader.FindNextFullScan(fullScan + 1, lastScanNumber)) != -1)
{
if (_rawReader.IsBadDataScan(fullScan))
{
continue;
}
scanNumber++;
var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber);
if (null == item)
{
break;
}
envelopes.Add(item);
}
//对每个scan计算轻重的离子丰度
envelopes.ForEach(m => m.CalculateIntensity(pkls.LightProfile, pkls.HeavyProfile));
pkls.Add(envelopes);
envelopeSpectrumGroup.Add(envelopes, new List <IIdentifiedSpectrum>());
envelopeSpectrumGroup[envelopes].Add(spectrum);
}
}
finally
{
_rawReader.Close();
}
foreach (string key in spectrumKeyMap.Keys)
{
DifferentRetentionTimeEnvelopes pkls = spectrumKeyMap[key];
foreach (SilacEnvelopes envelopes in pkls)
{
if (0 == envelopes.Count)
{
continue;
}
List <IIdentifiedSpectrum> mps = envelopeSpectrumGroup[envelopes];
double mzTolerance = PrecursorUtils.ppm2mz(mps[0].Query.ObservedMz, option.PPMTolerance);
string scanStr = GetScanRange(envelopes);
string resultFilename = detailDir + "\\" + mps[0].Query.FileScan.Experimental + "." + PeptideUtils.GetPureSequence(mps[0].Sequence) + "." + mps[0].Query.Charge + scanStr + ".silac";
IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(mps[0].GetMatchSequence(), mps[0].TheoreticalMH, mps[0].Query.Charge);
SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo);
SilacQuantificationSummaryItem item = new SilacQuantificationSummaryItem(sci.Light.IsSample);
item.RawFilename = rawFileName;
item.SoftwareVersion = this.SoftwareVersion;
item.PeptideSequence = mps[0].Sequence;
item.Charge = mps[0].Charge;
item.LightAtomComposition = sci.Light.Composition.ToString();
item.HeavyAtomComposition = sci.Heavy.Composition.ToString();
item.LightProfile = pkls.LightProfile;
item.HeavyProfile = pkls.HeavyProfile;
item.ObservedEnvelopes = envelopes;
item.ValidateScans(sci, precursorPPM);
item.Smoothing();
item.CalculateRatio();
new SilacQuantificationSummaryItemXmlFormat().WriteToFile(resultFilename, item);
int maxScoreItemIndex = FindMaxScoreItemIndex(mps);
for (int i = 0; i < mps.Count; i++)
{
if (maxScoreItemIndex == i)
{
item.AssignToAnnotation(mps[i], resultFilename);
}
else
{
item.AssignDuplicationToAnnotation(mps[i], resultFilename);
}
}
}
}
foreach (IIdentifiedSpectrum mph in spectra)
{
mph.InitializeRatioEnabled();
}
}
public SilacQuantificationSummaryItem ReadFromFile(string filename)
{
XElement root = XElement.Load(filename);
var result = new SilacQuantificationSummaryItem(root.GetChildValue("SampleIsLight", true));
result.RawFilename = root.GetChildValue("RawFilename", "");
result.SoftwareVersion = root.GetChildValue("SoftwareVersion", "");
result.PeptideSequence = root.GetChildValue("PeptideSequence");
result.Charge = root.GetChildValue("Charge", 2);
result.SampleAtomComposition = root.GetChildValue("SampleAtomComposition");
result.ReferenceAtomComposition = root.GetChildValue("ReferenceAtomComposition");
result.Ratio = root.GetChildValue("Ratio", 0.0);
result.RegressionCorrelation = root.GetChildValue("Correlation", 0.0);
result.SampleAbundance = root.GetChildValue("SampleAbundance", 0.0);
result.ReferenceAbundance = root.GetChildValue("ReferenceAbundance", 0.0);
result.SampleProfile = new List <Peak>();
ReadProfile(root, "SampleProfile", result.SampleProfile);
result.ReferenceProfile = new List <Peak>();
ReadProfile(root, "ReferenceProfile", result.ReferenceProfile);
var observed = root.Element("ObservedEnvelopes");
result.ObservedEnvelopes = new SilacEnvelopes();
foreach (var pkl in observed.Elements())
{
var peakList = new SilacPeakListPair();
int scan = Convert.ToInt32(pkl.Attribute("Scan").Value);
double retentiontime = MyConvert.ToDouble(pkl.Attribute("Retentiontime").Value);
peakList.Enabled = Convert.ToBoolean(pkl.Attribute("Enabled").Value);
peakList.IsIdentified = Convert.ToBoolean(pkl.Attribute("Identified").Value);
var extended = pkl.Attribute("ExtendedIdentification");
if (extended != null)
{
peakList.IsExtendedIdentification = Convert.ToBoolean(pkl.Attribute("ExtendedIdentification").Value);
}
else
{
peakList.IsExtendedIdentification = false;
}
peakList.LightIntensity = MyConvert.ToDouble(pkl.Attribute("LightIntensity").Value);
peakList.HeavyIntensity = MyConvert.ToDouble(pkl.Attribute("HeavyIntensity").Value);
peakList.Light = new PeakList <Peak>();
peakList.Light.ScanTimes.Add(new ScanTime(scan, retentiontime));
peakList.Heavy = new PeakList <Peak>();
peakList.Heavy.ScanTimes.Add(new ScanTime(scan, retentiontime));
ReadPeakList(pkl, "LightPeakList", peakList.Light);
ReadPeakList(pkl, "HeavyPeakList", peakList.Heavy);
result.ObservedEnvelopes.Add(peakList);
}
if (result.LightProfile[0].Mz == 0.0)
{
EmassProfileBuilder builder = new EmassProfileBuilder();
double minPercentage = 0.0001;
AtomComposition acSample = new AtomComposition(result.SampleAtomComposition);
result.SampleProfile = builder.GetProfile(acSample, result.Charge, minPercentage);
AtomComposition acRef = new AtomComposition(result.ReferenceAtomComposition);
result.ReferenceProfile = builder.GetProfile(acRef, result.Charge, minPercentage);
}
result.CalculateCorrelation();
return(result);
}
public SilacQuantificationSummaryItem ReadFromFile(string filename)
{
var doc = new XmlDocument();
doc.Load(filename);
XmlNode root = doc.DocumentElement;
var xmlHelper = new XmlHelper(doc);
var result = new SilacQuantificationSummaryItem(bool.Parse(xmlHelper.GetValidChild(root, "SampleIsLight").InnerText));
result.RawFilename = xmlHelper.GetValidChild(root, "RawFilename").InnerText;
XmlNode n = xmlHelper.GetFirstChild(root, "SoftwareVersion");
if (n != null)
{
result.SoftwareVersion = n.InnerText;
}
result.PeptideSequence = xmlHelper.GetValidChild(root, "PeptideSequence").InnerText;
result.Charge = Convert.ToInt32(xmlHelper.GetValidChild(root, "Charge").InnerText);
result.SampleAtomComposition = xmlHelper.GetValidChild(root, "SampleAtomComposition").InnerText;
result.ReferenceAtomComposition = xmlHelper.GetValidChild(root, "ReferenceAtomComposition").InnerText;
result.Ratio = MyConvert.ToDouble(xmlHelper.GetValidChild(root, "Ratio").InnerText);
result.RegressionCorrelation = MyConvert.ToDouble(xmlHelper.GetValidChild(root, "Correlation").InnerText);
result.SampleAbundance = MyConvert.ToDouble(xmlHelper.GetValidChild(root, "SampleAbundance").InnerText);
result.ReferenceAbundance = MyConvert.ToDouble(xmlHelper.GetValidChild(root, "ReferenceAbundance").InnerText);
result.SampleProfile = new List <Peak>();
ReadProfile(xmlHelper, root, "SampleProfile", result.SampleProfile);
result.ReferenceProfile = new List <Peak>();
ReadProfile(xmlHelper, root, "ReferenceProfile", result.ReferenceProfile);
XmlNode observed = xmlHelper.GetValidChild(root, "ObservedEnvelopes");
result.ObservedEnvelopes = new SilacEnvelopes();
foreach (XmlNode pkl in observed.ChildNodes)
{
var peakList = new SilacPeakListPair();
int scan = int.Parse(pkl.Attributes["Scan"].InnerText);
double retentiontime = MyConvert.ToDouble(pkl.Attributes["Retentiontime"].InnerText);
peakList.Enabled = bool.Parse(pkl.Attributes["Enabled"].InnerText);
peakList.IsIdentified = bool.Parse(pkl.Attributes["Identified"].InnerText);
var extended = pkl.Attributes["ExtendedIdentification"];
if (extended != null)
{
peakList.IsExtendedIdentification = bool.Parse(pkl.Attributes["ExtendedIdentification"].InnerText);
}
else
{
peakList.IsExtendedIdentification = false;
}
peakList.LightIntensity = MyConvert.ToDouble(pkl.Attributes["LightIntensity"].InnerText);
peakList.HeavyIntensity = MyConvert.ToDouble(pkl.Attributes["HeavyIntensity"].InnerText);
peakList.Light = new PeakList <Peak>();
peakList.Light.ScanTimes.Add(new ScanTime(scan, retentiontime));
peakList.Heavy = new PeakList <Peak>();
peakList.Heavy.ScanTimes.Add(new ScanTime(scan, retentiontime));
ReadPeakList(xmlHelper, pkl, "LightPeakList", peakList.Light);
ReadPeakList(xmlHelper, pkl, "HeavyPeakList", peakList.Heavy);
result.ObservedEnvelopes.Add(peakList);
}
result.CalculateCorrelation();
return(result);
}