io.github.msdk.datamodel

Interface MsScan

All Superinterfaces:

MsSpectrum

All Known Implementing Classes:

MzMLMsScan, NetCDFMsScan, SimpleMsScan

public interface MsScan
extends MsSpectrum

Represents a single MS scan in a raw data file. This interface extends MsSpectrum, therefore the actual data points can be accessed through the inherited methods of MsSpectrum. If the scan is not added to any file, its data points are stored in memory. However, once the scan is added into a raw data file by calling setRawDataFile(), its data points will be stored in a temporary file that belongs to that RawDataFile. When RawDataFile.dispose() is called, the data points are discarded so the MsScan instance cannot be used anymore.

Method Summary

Modifier and Type	Method and Description
List<IsolationInfo>	getIsolations() Returns a list of isolations performed for this scan.
String	getMsFunction() Returns the MS function of this scan, e.g.
Integer	getMsLevel() Returns MS level (1 = default, 2 = MS/MS, 3 = MS3 etc.).
default MsScanType	getMsScanType() Returns the type of the MS scan.
default PolarityType	getPolarity() Returns the polarity of this scan.
RawDataFile	getRawDataFile() Returns the raw data file that contains this scan.
Float	getRetentionTime() Returns the retention time in seconds
String	getScanDefinition() Returns the instrument-specific textual definition of the scan parameters.
com.google.common.collect.Range<Double>	getScanningRange() Returns the scanning range of the instrument.
Integer	getScanNumber() Returns the number of this scan, represented by an integer, typically positive.
ActivationInfo	getSourceInducedFragmentation() Returns the fragmentation parameters of ion source-induced fragmentation, or null if no such information is known.

Methods inherited from interface io.github.msdk.datamodel.MsSpectrum

getIntensityValues, getIntensityValues, getMzRange, getMzTolerance, getMzValues, getMzValues, getNumberOfDataPoints, getSpectrumType, getTIC

Method Detail

getRawDataFile

@Nullable
RawDataFile getRawDataFile()

Returns the raw data file that contains this scan. This might return null when the scan is created, but once the scan is added to the raw data file by calling RawDataFile.addScan(), the RawDataFile automatically calls the MsScan.setRawDataFile() method to update this reference.

Returns:

RawDataFile containing this MsScan, or null.

See Also:

RawDataFile

getScanNumber

@Nonnull
Integer getScanNumber()

Returns the number of this scan, represented by an integer, typically positive. Typically, the scan number will be unique within the file. However, the data model does not guarantee that, and in some cases multiple scans with the same number may be present in the file.

Returns:

Scan number

getScanDefinition

@Nullable
String getScanDefinition()

Returns the instrument-specific textual definition of the scan parameters. For example, in Thermo raw data this may look like: FTMS + p ESI Full ms2 209.09@hcd35.00 [50.00-230.00] The scan definition can be null if not specified in the raw data.

Returns:

Scan definition

getMsFunction

@Nullable
String getMsFunction()

Returns the MS function of this scan, e.g. "Full ms", or "SRM".

Returns:

MS function.

getMsLevel

@Nonnull
Integer getMsLevel()

Returns MS level (1 = default, 2 = MS/MS, 3 = MS3 etc.).

Returns:

MS level

getMsScanType

@Nonnull
default MsScanType getMsScanType()

Returns the type of the MS scan. If unknown, MsScanType.UNKNOWN is returned.

Returns:

MS scan type

getRetentionTime

@Nullable
Float getRetentionTime()

Returns the retention time in seconds

Returns:

RT

getScanningRange

@Nullable
com.google.common.collect.Range<Double> getScanningRange()

Returns the scanning range of the instrument. Note that this value is different from that returned by getMzRange() from the MassSpectrum interface. getMzRange() returns the range of the actual data points (lowest and highest m/z) getScanningRange() returns the instrument scanning range that was configured in the experiment setup.

Returns:

The scanning m/z range of the instrument

getPolarity

@Nonnull
default PolarityType getPolarity()

Returns the polarity of this scan. If unknown, PolarityType.UNKNOWN is returned.

Returns:

Polarity of this scan.

getSourceInducedFragmentation

@Nullable
ActivationInfo getSourceInducedFragmentation()

Returns the fragmentation parameters of ion source-induced fragmentation, or null if no such information is known.

Returns:

Fragmentation info of ion source-induced fragmentation, or null.

getIsolations

@Nonnull
List<IsolationInfo> getIsolations()

Returns a list of isolations performed for this scan. These isolations may also include fragmentations (tandem MS).

Returns:

A mutable list of isolations. New isolation items can be added to this list.