OpenMS
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Extracts individual channels from MS/MS spectra for isobaric labeling experiments. More...
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.h>
Classes | |
struct | PuritySate_ |
Small struct to capture the current state of the purity computation. More... | |
Public Member Functions | |
IsobaricChannelExtractor (const IsobaricQuantitationMethod *const quant_method) | |
C'tor to create a new channel extractor for the given quantitation method. More... | |
IsobaricChannelExtractor (const IsobaricChannelExtractor &other) | |
Copy c'tor. More... | |
IsobaricChannelExtractor & | operator= (const IsobaricChannelExtractor &rhs) |
Assignment operator. More... | |
void | extractChannels (const PeakMap &ms_exp_data, ConsensusMap &consensus_map) |
Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map. More... | |
Public Member Functions inherited from DefaultParamHandler | |
DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Protected Member Functions | |
void | setDefaultParams_ () |
implemented for DefaultParamHandler More... | |
void | updateMembers_ () override |
implemented for DefaultParamHandler More... | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Private Member Functions | |
void | registerChannelsInOutputMap_ (ConsensusMap &consensus_map) |
add channel information to the map after it has been filled More... | |
bool | isValidPrecursor_ (const Precursor &precursor) const |
Checks if the given precursor fulfills all constraints for extractions. More... | |
bool | hasLowIntensityReporter_ (const ConsensusFeature &cf) const |
Checks whether the given ConsensusFeature contains a channel that is below the given intensity threshold. More... | |
double | computePrecursorPurity_ (const PeakMap::ConstIterator &ms2_spec, const PuritySate_ &precursor) const |
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum. More... | |
double | computeSingleScanPrecursorPurity_ (const PeakMap::ConstIterator &ms2_spec, const PeakMap::SpectrumType &precursor_spec) const |
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and a reference to the potential precursor spectrum. More... | |
String | getActivationMethod_ (const PeakMap::SpectrumType &s) const |
Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum. More... | |
Private Attributes | |
const IsobaricQuantitationMethod * | quant_method_ |
The used quantitation method (itraq4plex, tmt6plex,..). More... | |
String | selected_activation_ |
Used to select only specific types of spectra for the channel extraction. More... | |
Peak2D::CoordinateType | reporter_mass_shift_ |
Allowed deviation between the expected and observed reporter ion m/z. More... | |
Peak2D::IntensityType | min_precursor_intensity_ |
Minimum intensity of the precursor to be considered for quantitation. More... | |
bool | keep_unannotated_precursor_ |
Flag if precursor with missing intensity value or missing precursor spectrum should be included or not. More... | |
Peak2D::IntensityType | min_reporter_intensity_ |
Minimum reporter ion intensity to be considered for quantitation. More... | |
bool | remove_low_intensity_quantifications_ |
Flag if complete quantification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ . More... | |
double | min_precursor_purity_ |
Minimum precursor purity to accept the spectrum for quantitation. More... | |
double | max_precursor_isotope_deviation_ |
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor. More... | |
bool | interpolate_precursor_purity_ |
Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan. More... | |
Additional Inherited Members | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
Writes all parameters to meta values. More... | |
Protected Attributes inherited from DefaultParamHandler | |
Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
In addition to extracting the channel information this class can also filter the extracted channel information according to several parameters, i.e., discard channel information if certain criteria are not met.
The precursor purity computation uses the interpolation approach described in: Savitski MM, Sweetman G, Askenazi M, et al. (2011). Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers. Analytical chemistry 83: 8959-67. http://www.ncbi.nlm.nih.gov/pubmed/22017476
Name | Type | Default | Restrictions | Description |
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select_activation | string | auto | auto, Collision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, Electron transfer and collision-induced dissociation, Electron transfer and higher-energy collision dissociation, Pulsed q dissociation, trap-type collision-induced dissociation, beam-type collision-induced dissociation, in-source collision-induced dissociation, any | Operate only on MSn scans where any of its precursors features a certain activation method. Setting to "auto" uses HCD and HCID spectra. Set to empty string if you want to disable filtering. |
reporter_mass_shift | float | 2.0e-03 | min: 1.0e-04 max: 0.5 | Allowed shift (left to right) in Th from the expected position. |
min_precursor_intensity | float | 1.0 | min: 0.0 | Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation. |
keep_unannotated_precursor | string | true | true, false | Flag if precursor with missing intensity value or missing precursor spectrum should be included or not. |
min_reporter_intensity | float | 0.0 | min: 0.0 | Minimum intensity of the individual reporter ions to be extracted. |
discard_low_intensity_quantifications | string | false | true, false | Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'. |
min_precursor_purity | float | 0.0 | min: 0.0 max: 1.0 | Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor. |
precursor_isotope_deviation | float | 10.0 | min: 0.0 | Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor. |
purity_interpolation | string | true | true, false | If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan. If set to false, only the precursor scan will be used. |
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explicit |
C'tor to create a new channel extractor for the given quantitation method.
quant_method | IsobaricQuantitationMethod providing the necessary information which channels should be extracted. |
IsobaricChannelExtractor | ( | const IsobaricChannelExtractor & | other | ) |
Copy c'tor.
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private |
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum.
ms2_spec | Iterator pointing to the MS2 spectrum. |
precursor | Iterator pointing to the precursor spectrum of ms2_spec. |
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private |
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and a reference to the potential precursor spectrum.
ms2_spec | Iterator pointing to the MS2 spectrum. |
precursor_spec | Precursor spectrum of ms2_spec. |
void extractChannels | ( | const PeakMap & | ms_exp_data, |
ConsensusMap & | consensus_map | ||
) |
Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map.
ms_exp_data | Raw data to search for isobaric quantitation channels. |
consensus_map | Output map containing the identified channels and the corresponding intensities. |
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inlineprivate |
Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.
s | The spectrum |
References SpectrumSettings::getPrecursors(), and Precursor::NamesOfActivationMethod.
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private |
Checks whether the given ConsensusFeature contains a channel that is below the given intensity threshold.
cf | The ConsensusFeature to check. |
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private |
Checks if the given precursor fulfills all constraints for extractions.
precursor | The precursor to test. |
IsobaricChannelExtractor& operator= | ( | const IsobaricChannelExtractor & | rhs | ) |
Assignment operator.
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private |
add channel information to the map after it has been filled
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protected |
implemented for DefaultParamHandler
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overrideprotectedvirtual |
implemented for DefaultParamHandler
Reimplemented from DefaultParamHandler.
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private |
Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan.
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private |
Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.
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private |
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.
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private |
Minimum intensity of the precursor to be considered for quantitation.
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private |
Minimum precursor purity to accept the spectrum for quantitation.
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private |
Minimum reporter ion intensity to be considered for quantitation.
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private |
The used quantitation method (itraq4plex, tmt6plex,..).
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private |
Flag if complete quantification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ .
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private |
Allowed deviation between the expected and observed reporter ion m/z.
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private |
Used to select only specific types of spectra for the channel extraction.