/// <summary>
/// Handle a single precursor element and child nodes
/// Called by ReadPrecursorList (xml hierarchy)
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope of the single precursor element</param>
/// <returns></returns>
private Precursor ReadPrecursor(XmlReader reader)
{
reader.MoveToContent();
reader.ReadStartElement("precursor"); // Throws exception if we are not at the "precursor" tag.
XmlReader innerReader;
Precursor precursor = new Precursor();
while (reader.ReadState == ReadState.Interactive)
{
// Handle exiting out properly at EndElement tags
if (reader.NodeType != XmlNodeType.Element)
{
reader.Read();
continue;
}
switch (reader.Name)
{
case "isolationWindow":
// Schema requirements: zero to one instances of this element
innerReader = reader.ReadSubtree();
innerReader.MoveToContent();
innerReader.ReadStartElement("isolationWindow"); // Throws exception if we are not at the "selectedIon" tag.
while (innerReader.ReadState == ReadState.Interactive)
{
// Handle exiting out properly at EndElement tags
if (innerReader.NodeType != XmlNodeType.Element)
{
innerReader.Read();
continue;
}
switch (innerReader.Name)
{
case "referenceableParamGroupRef":
// Schema requirements: zero to many instances of this element
innerReader.Skip();
break;
case "cvParam":
// Schema requirements: zero to many instances of this element
/* MUST supply a *child* term of MS:1000792 (isolation window attribute) one or more times
* e.g.: MS:1000827 (isolation window target m/z)
* e.g.: MS:1000828 (isolation window lower offset)
* e.g.: MS:1000829 (isolation window upper offset)
*/
switch (innerReader.GetAttribute("accession"))
{
case "MS:1000827":
// name="isolation window target m/z"
precursor.IsolationWindowTargetMz = Convert.ToDouble(innerReader.GetAttribute("value"));
break;
case "MS:1000828":
// name="isolation window lower offset"
precursor.IsolationWindowLowerOffset = Convert.ToDouble(innerReader.GetAttribute("value"));
break;
case "MS:1000829":
// name="isolation window upper offset"
precursor.IsolationWindowUpperOffset = Convert.ToDouble(innerReader.GetAttribute("value"));
break;
}
innerReader.Read(); // Consume the cvParam element (no child nodes)
break;
case "userParam":
// Schema requirements: zero to many instances of this element
innerReader.Skip();
break;
default:
innerReader.Skip();
break;
}
}
innerReader.Close();
reader.Read(); // "selectedIon" might not have child nodes
// We will either consume the EndElement, or the same element that was passed to ReadSpectrum (in case of no child nodes)
break;
case "selectedIonList":
// Schema requirements: zero to one instances of this element
// mzML_1.0.0: one instance of this element
precursor.Ions = ReadSelectedIonList(reader.ReadSubtree());
reader.ReadEndElement(); // "selectedIonList" must have child nodes
break;
case "activation":
// Schema requirements: one instance of this element
innerReader = reader.ReadSubtree();
innerReader.MoveToContent();
innerReader.ReadStartElement("activation"); // Throws exception if we are not at the "activation" tag.
while (innerReader.ReadState == ReadState.Interactive)
{
// Handle exiting out properly at EndElement tags
if (innerReader.NodeType != XmlNodeType.Element)
{
innerReader.Read();
continue;
}
switch (innerReader.Name)
{
case "referenceableParamGroupRef":
// Schema requirements: zero to many instances of this element
innerReader.Skip();
break;
case "cvParam":
// Schema requirements: zero to many instances of this element
/* MAY supply a *child* term of MS:1000510 (precursor activation attribute) one or more times
* e.g.: MS:1000045 (collision energy)
* e.g.: MS:1000138 (percent collision energy)
* e.g.: MS:1000245 (charge stripping)
* e.g.: MS:1000412 (buffer gas)
* e.g.: MS:1000419 (collision gas)
* e.g.: MS:1000509 (activation energy)
* e.g.: MS:1000869 (collision gas pressure)
* MUST supply term MS:1000044 (dissociation method) or any of its children one or more times
* e.g.: MS:1000133 (collision-induced dissociation)
* e.g.: MS:1000134 (plasma desorption)
* e.g.: MS:1000135 (post-source decay)
* e.g.: MS:1000136 (surface-induced dissociation)
* e.g.: MS:1000242 (blackbody infrared radiative dissociation)
* e.g.: MS:1000250 (electron capture dissociation)
* e.g.: MS:1000262 (infrared multiphoton dissociation)
* e.g.: MS:1000282 (sustained off-resonance irradiation)
* e.g.: MS:1000422 (high-energy collision-induced dissociation)
* e.g.: MS:1000433 (low-energy collision-induced dissociation)
* et al.
*
* e.g.: MS:1000133 "collision-induced dissociation"
* e.g.: MS:1000134 "plasma desorption"
* e.g.: MS:1000135 "post-source decay"
* e.g.: MS:1000136 "surface-induced dissociation"
* e.g.: MS:1000242 "blackbody infrared radiative dissociation"
* e.g.: MS:1000250 "electron capture dissociation"
* e.g.: MS:1000262 "infrared multiphoton dissociation"
* e.g.: MS:1000282 "sustained off-resonance irradiation"
* e.g.: MS:1000422 "beam-type collision-induced dissociation"
* e.g.: MS:1000433 "low-energy collision-induced dissociation"
* e.g.: MS:1000435 "photodissociation"
* e.g.: MS:1000598 "electron transfer dissociation"
* e.g.: MS:1000599 "pulsed q dissociation"
* e.g.: MS:1001880 "in-source collision-induced dissociation"
* e.g.: MS:1002000 "LIFT"
* e.g.: MS:1002472 "trap-type collision-induced dissociation"
*/
switch (innerReader.GetAttribute("accession"))
{
case "MS:1000133":
// name="collision-induced dissociation"
precursor.Activation = ActivationMethod.CID;
break;
case "MS:1000598":
// name="electron transfer dissociation"
precursor.Activation = ActivationMethod.ETD;
break;
case "MS:1000422":
// name="beam-type collision-induced dissociation", "high-energy collision-induced dissociation"
precursor.Activation = ActivationMethod.HCD;
break;
case "MS:1000250":
// name="electron capture dissociation"
precursor.Activation = ActivationMethod.ECD;
break;
case "MS:1000599":
// name="pulsed q dissociation"
precursor.Activation = ActivationMethod.PQD;
break;
case "MS:1000045":
// name="collision energy"
//energy = Convert.ToDouble(innerReader.GetAttribute("value"));
break;
}
innerReader.Read(); // Consume the cvParam element (no child nodes)
break;
case "userParam":
// Schema requirements: zero to many instances of this element
innerReader.Skip();
break;
default:
innerReader.Skip();
break;
}
}
innerReader.Close();
reader.Read(); // "selectedIon" might not have child nodes
// We will either consume the EndElement, or the same element that was passed to ReadSpectrum (in case of no child nodes)
break;
default:
reader.Skip();
break;
}
}
reader.Close();
return precursor;
}
/// <summary>
/// Handle a single spectrum element and child nodes
/// Called by ReadSpectrumList (xml hierarchy)
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope of the single spectrum element</param>
/// <param name="includePeaks">Whether to read binary data arrays</param>
private Spectrum ReadSpectrum(XmlReader reader, bool includePeaks = true)
{
reader.MoveToContent();
string index = reader.GetAttribute("index");
//Console.WriteLine("Reading spectrum indexed by " + index);
// This is correct for Thermo files converted by msConvert, but need to implement for others as well
string spectrumId = reader.GetAttribute("id"); // Native ID in mzML_1.1.0; unique identifier in mzML_1.0.0, often same as nativeID
string nativeId = spectrumId;
if (_version == MzML_Version.mzML1_0_0)
{
nativeId = reader.GetAttribute("nativeID"); // Native ID in mzML_1.0.0
}
int scanNum = -1;
// If a random access reader, there is already a scan number stored, based on the order of the index. Use it instead.
if (_randomAccess)
{
scanNum = (int) (_spectrumOffsets.NativeToIdMap[nativeId]);
}
else
{
scanNum = (int)(_artificialScanNum++);
// Interpret the NativeID (if the format has an interpreter) and use it instead of the artificial number.
// TODO: Better handling than the artificial ID for other nativeIDs (ones currently not supported)
int num = 0;
if (NativeIdConversion.TryGetScanNumberInt(nativeId, out num))
{
scanNum = num;
}
}
int defaultArraySize = Convert.ToInt32(reader.GetAttribute("defaultArrayLength"));
reader.ReadStartElement("spectrum"); // Throws exception if we are not at the "spectrum" tag.
bool is_ms_ms = false;
int msLevel = 0;
bool centroided = false;
double tic = 0;
List<Precursor> precursors = new List<Precursor>();
List<ScanData> scans = new List<ScanData>();
List<BinaryDataArray> bdas = new List<BinaryDataArray>();
while (reader.ReadState == ReadState.Interactive)
{
// Handle exiting out properly at EndElement tags
if (reader.NodeType != XmlNodeType.Element)
{
reader.Read();
continue;
}
//////////////////////////////////////////////////////////////////////////////////////
///
/// MS1 Spectra: only need Spectrum data: scanNum, MSLevel, ElutionTime, mzArray, IntensityArray
///
/// MS2 Spectra: use ProductSpectrum; adds ActivationMethod and IsolationWindow
///
//////////////////////////////////////////////////////////////////////////////////////
switch (reader.Name)
{
case "referenceableParamGroupRef":
// Schema requirements: zero to many instances of this element
reader.Skip();
break;
case "cvParam":
// Schema requirements: zero to many instances of this element
/* MAY supply a *child* term of MS:1000465 (scan polarity) only once
* e.g.: MS:1000129 (negative scan)
* e.g.: MS:1000130 (positive scan)
* MUST supply a *child* term of MS:1000559 (spectrum type) only once
* e.g.: MS:1000322 (charge inversion mass spectrum)
* e.g.: MS:1000325 (constant neutral gain spectrum)
* e.g.: MS:1000326 (constant neutral loss spectrum)
* e.g.: MS:1000328 (e/2 mass spectrum)
* e.g.: MS:1000341 (precursor ion spectrum)
* e.g.: MS:1000579 (MS1 spectrum)
* e.g.: MS:1000580 (MSn spectrum)
* e.g.: MS:1000581 (CRM spectrum)
* e.g.: MS:1000582 (SIM spectrum)
* e.g.: MS:1000583 (SRM spectrum)
* e.g.: MS:1000620 (PDA spectrum)
* e.g.: MS:1000627 (selected ion current chromatogram)
* e.g.: MS:1000789 (enhanced multiply charged spectrum)
* e.g.: MS:1000790 (time-delayed fragmentation spectrum)
* et al.
* MUST supply term MS:1000525 (spectrum representation) or any of its children only once
* e.g.: MS:1000127 (centroid spectrum)
* e.g.: MS:1000128 (profile spectrum)
* MAY supply a *child* term of MS:1000499 (spectrum attribute) one or more times
* e.g.: MS:1000285 (total ion current)
* e.g.: MS:1000497 (zoom scan)
* e.g.: MS:1000504 (base peak m/z)
* e.g.: MS:1000505 (base peak intensity)
* e.g.: MS:1000511 (ms level)
* e.g.: MS:1000527 (highest observed m/z)
* e.g.: MS:1000528 (lowest observed m/z)
* e.g.: MS:1000618 (highest observed wavelength)
* e.g.: MS:1000619 (lowest observed wavelength)
* e.g.: MS:1000796 (spectrum title)
* et al.
*/
switch (reader.GetAttribute("accession"))
{
case "MS:1000127":
// name="centroid spectrum"
centroided = true;
break;
case "MS:1000128":
// name="profile spectrum"
centroided = false;
break;
case "MS:1000511":
// name="ms level"
msLevel = Convert.ToInt32(reader.GetAttribute("value"));
break;
case "MS:1000579":
// name="MS1 spectrum"
is_ms_ms = false;
break;
case "MS:1000580":
// name="MSn spectrum"
is_ms_ms = true;
break;
case "MS:1000285":
// name="total ion current"
tic = Convert.ToDouble(reader.GetAttribute("value"));
break;
}
reader.Read(); // Consume the cvParam element (no child nodes)
break;
case "userParam":
// Schema requirements: zero to many instances of this element
reader.Skip();
break;
case "spectrumDescription": // mzML_1.0.0 compatibility
// Schema requirements: one instance of this element
ReadSpectrumDescription(reader.ReadSubtree(), ref scans, ref precursors, out centroided);
reader.ReadEndElement(); // "spectrumDescription" must have child nodes
break;
case "scanList":
// Schema requirements: zero to one instances of this element
scans.AddRange(ReadScanList(reader.ReadSubtree()));
reader.ReadEndElement(); // "scanList" must have child nodes
break;
case "precursorList":
// Schema requirements: zero to one instances of this element
precursors.AddRange(ReadPrecursorList(reader.ReadSubtree()));
reader.ReadEndElement(); // "precursorList" must have child nodes
break;
case "productList":
// Schema requirements: zero to one instances of this element
reader.Skip();
break;
case "binaryDataArrayList":
// Schema requirements: zero to one instances of this element
if (includePeaks)
{
bdas.AddRange(ReadBinaryDataArrayList(reader.ReadSubtree(), defaultArraySize));
reader.ReadEndElement(); // "binaryDataArrayList" must have child nodes
}
else
{
reader.Skip();
}
break;
default:
reader.Skip();
break;
}
}
reader.Close();
// Process the spectrum data
ScanData scan = new ScanData();
Spectrum spectrum;
BinaryDataArray mzs = new BinaryDataArray();
BinaryDataArray intensities = new BinaryDataArray();
foreach (var bda in bdas)
{
if (bda.ArrayType == ArrayType.m_z_array)
{
mzs = bda;
}
else if (bda.ArrayType == ArrayType.intensity_array)
{
intensities = bda;
}
}
if (!centroided && includePeaks)
{
// Centroid spectrum
// ProteoWizard
var centroider = new Centroider(mzs.Data, intensities.Data);
double[] centroidedMzs, centroidedIntensities;
centroider.GetCentroidedData(out centroidedMzs, out centroidedIntensities);
mzs.Data = centroidedMzs;
intensities.Data = centroidedIntensities;
}
if (scans.Count == 1)
{
scan = scans[0];
}
else if (scans.Count > 1)
{
// TODO: Should do something else to appropriately handle combinations...
scan = scans[0];
}
if (is_ms_ms)
{
Precursor precursor = new Precursor();
if (precursors.Count == 1)
{
precursor = precursors[0];
}
else if (precursors.Count > 1)
{
// TODO: Should do something else to appropriately handle multiple precursors...
precursor = precursors[0];
}
SelectedIon ion = new SelectedIon();
if (precursor.Ions.Count == 1)
{
ion = precursor.Ions[0];
}
else if (precursor.Ions.Count > 1)
{
// TODO: Should do something else to appropriately handle multiple selected ions...
ion = precursor.Ions[0];
}
var pspectrum = new ProductSpectrum(mzs.Data, intensities.Data, scanNum);
pspectrum.ActivationMethod = precursor.Activation;
// Select mz value to use based on presence of a Thermo-specific user param.
// The user param has a slightly higher precision, if that matters.
double mz = scan.MonoisotopicMz == 0.0 ? ion.SelectedIonMz : scan.MonoisotopicMz;
pspectrum.IsolationWindow = new IsolationWindow(precursor.IsolationWindowTargetMz, precursor.IsolationWindowLowerOffset, precursor.IsolationWindowUpperOffset, mz, ion.Charge);
//pspectrum.IsolationWindow.OldCharge = ion.OldCharge;
//pspectrum.IsolationWindow.SelectedIonMz = ion.SelectedIonMz;
spectrum = pspectrum;
}
else
{
spectrum = new Spectrum(mzs.Data, intensities.Data, scanNum);
}
spectrum.MsLevel = msLevel;
spectrum.ElutionTime = scan.StartTime;
spectrum.NativeId = nativeId;
spectrum.TotalIonCurrent = tic;
return spectrum;
}