Spectrum

Remarks

A spectrum of basic m/z and intensity data points. It is TSpectrum<SpecDataPoint>.

Implements

ISpectrum<SpecDataPoint>, IDisposable

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Constructors

Syntax	Description
Spectrum(int count = 0)	Creates a spectrum sized for the given number of data points.

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Properties

Inherited from TSpectrum<T>

Identifier	Type	Description
Count	int	The number of data points. Stored rather than computed from DataPoints.Length, for speed.
DataPoints	SpecDataPoint[]	The data points. Assigning a new array here directly does not update Count; use Resize.

Inherited from SpectrumFoundation

Identifier	Type	Description
Analyzer	string	Mass analyzer used.
BasePeakIntensity	double	The abundance of the most intense peak in the scan.
BasePeakMz	double	The m/z of the most intense peak in the scan.
Centroid	bool	Identifies the peak data type as centroid (true) or profile (false).
CollisionEnergy	double	The activation energy for a fragmentation event.
Description	string	The “Scan Description” field from the scan header.
DetectorType	string	Detector or mass analyzer used for the scan, such as ITMS or FTMS.
ElapsedScanTime	double	Total time, including injection time, to acquire the scan, in milliseconds.
EndMz	double	m/z that the scan ends at.
FaimsCV	double	FAIMS compensation voltage, if used, in volts.
FaimsState	bool	FAIMS state, true when on. FaimsState can be on while FaimsCV is 0.
HighestMz	double	Highest m/z observed in the scan.
IonInjectionTime	double	Injection time used to acquire the scan ions, in milliseconds, maximum 5000.
LowestMz	double	Lowest m/z observed in the scan.
MasterIndex	int	Thermo variable for master scan number.
MetaData	Dictionary<string, string>	Key/value dictionary for information without a dedicated field.
MsLevel	int	The MS level: 0 unknown, 1 MS1, 2 MS2, 3 MS3, and so on.
Polarity	bool	Polarity, true when positive.
PrecursorActivationMethod	string	If a dependent scan, the activation method used to generate the scan fragments.
PrecursorMasterScanNumber	int	If a dependent scan, the parent scan number.
Precursors	List<PrecursorIon>	Zero or more precursor ions associated with this spectrum.
RetentionTime	double	Scan retention time, in minutes.
ScanDescription	string	The scan description.
ScanEvent	int	Scan event order.
ScanFilter	string	Scan filter line from the raw file.
ScanNumber	int	Scan number.
ScanType	string	String description of the scan type.
StartMz	double	m/z that the scan starts at.
TotalIonCurrent	double	Total ion current for the scan.

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Methods

Inherited from TSpectrum<T>

Method	Returns	Description
Deserialize(byte[] data)	void	Reads a byte array into spectrum object data members.
Dispose()	void	A no-op beyond marking the instance disposed; a spectrum holds no unmanaged resources.
GetMz(double mz, double ppm = 0)	int	Finds the data point at an m/z, or the nearest one within a tolerance.
Resize(int sz)	void	Replaces the data points with a new, empty array of the given size. Existing points are discarded.
Serialize()	byte[]	Writes spectrum object data members into a byte array. Not every member is carried.

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Example

using Nova.Data;
using Nova.Io.Read;

int ms1Count = 0;
int ms2Count = 0;
FileReader reader = new FileReader("TheBestDataEver.mzML", MSFilter.MS1 | MSFilter.MS2);
foreach (Spectrum spec in reader)
{
  if (spec.MsLevel == 1)
  {
    ms1Count++;
  }
  else
  {
    ms2Count++;
  }
}
Console.WriteLine("There are " + ms1Count + " MS scans and " + ms2Count + " MS/MS scans.");