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OpenMS
2.8.0
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This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models. More...
#include <OpenMS/IONMOBILITY/IMDataConverter.h>
Static Public Member Functions | |
| static std::vector< PeakMap > | splitByFAIMSCV (PeakMap &&exp) |
| Splits a PeakMap into one PeakMap per FAIMS compensation voltage. More... | |
| static MSExperiment | splitByIonMobility (MSSpectrum im_frame, UInt number_of_bins=-1) |
| Split a (TimsTOF) ion mobility frame (i.e. a spectrum concatenated from multiple spectra with different IM values) into separate spectra. More... | |
| static MSExperiment | splitByIonMobility (MSExperiment &&in, UInt number_of_bins=-1) |
| Expands all (TimsTOF) ion mobility frames in the PeakMap (i.e. all IM spectra with an IM float data array) into separate spectra. Non-IM spectra are simply copied to the result. More... | |
| static MSExperiment | collapseFramesToSingle (const MSExperiment &in) |
| Collapses multiple MS spectra (each with its own drift time) from the same IM-frame into a single MSSpectrum (with an IM-float data array) More... | |
| static void | setIMUnit (DataArrays::FloatDataArray &fda, const DriftTimeUnit unit) |
| Convert from a Unit to a CV term and annotate is as the FDA's name. This is not very accurate (since we cannot decide if its 'raw' or 'binned' IM data), but it allows to reconstruct the unit from the IM float-data array which is annotated with this term. More... | |
| static bool | getIMUnit (const DataArrays::FloatDataArray &fda, DriftTimeUnit &unit) |
Checks if the fda is an ion-mobility array and if so, returns the unit (either MILLISECOND or VSSC, or NONE) More... | |
This class converts PeakMaps and MSSpectra from/to different IM/FAIMS storage models.
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Collapses multiple MS spectra (each with its own drift time) from the same IM-frame into a single MSSpectrum (with an IM-float data array)
Frames are recognized by having the same RT for subsequent spectra. The IM information is taken from each input spectrum's .getDriftTime(). Multiple frames are allowed. If the input already contains IM-frames, they are simply copied.
If a spectrum does not have drift time (spec.getDriftTime()), it is simply copied to the output and ignored during the collapsing process.
| exp | The input experiment with multiple spectra per frame |
| result | The output spectra collapsed to a single spectrum per frame |
| Exception::InvalidValue | if any spectrum has both a single drift time AND a IM-float data array (see IMTypes::determineIMFormat) |
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Checks if the fda is an ion-mobility array and if so, returns the unit (either MILLISECOND or VSSC, or NONE)
The name of the fda should correspond to a value set by setIMUnit(), but all CV names of child terms of 'MS:1002893 ! ion mobility array' are accepted.
| CV term | Unit |
|---|---|
| MS:1002816 ! mean ion mobility array | DriftTimeUnit::MILLISECOND |
| MS:1003008 ! raw inverse reduced ion mobility array | DriftTimeUnit::VSSC |
| MS:1002893 ! ion mobility array ** | DriftTimeUnit::NONE |
**) or a child term, which is not one of the terms used above.
| [in] | fda | Input array, which is tested for its name |
| [out] | unit | If fda is an IM array, the unit will contain the IM unit (undefined otherwise) |
fda is an IM array, false otherwise
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Convert from a Unit to a CV term and annotate is as the FDA's name. This is not very accurate (since we cannot decide if its 'raw' or 'binned' IM data), but it allows to reconstruct the unit from the IM float-data array which is annotated with this term.
| Unit | CV term |
|---|---|
| DriftTimeUnit::MILLISECOND | MS:1002816 ! mean ion mobility array |
| DriftTimeUnit::VSSC | MS:1003008 ! raw inverse reduced ion mobility array |
For any other unit (e.g. FAIMS-Compensation voltage) we throw, since the PSI CV does not (and should not?) have CV terms for other IM units in ion mobility arrays.
| [out] | fda | The FDA to be annotated as an IM array |
| [in] | unit | The unit of the IM measurement |
| Exception::InvalidValue | for unsupported units |
Splits a PeakMap into one PeakMap per FAIMS compensation voltage.
This only works with a PeakMap that has a FAIMS compensation voltage associated with each spectrum. The spectra from the original PeakMap are moved to new PeakMaps, so the original PeakMap is unusable afterwards.
| exp | The PeakMap |
| Exception::MissingInformation | if exp is not FAIMS data |
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Expands all (TimsTOF) ion mobility frames in the PeakMap (i.e. all IM spectra with an IM float data array) into separate spectra. Non-IM spectra are simply copied to the result.
To get some coarser custom binning, choose a smaller number_of_bins. The default creates a new bin (=spectrum in the output) for each distinct ion mobility value. For custom bins, the IM range is divided into equally spaced bins and the bin center is the new drift time.
| in | The PeakMap containing IM-frame spectra |
| number_of_bins | In how many bins should the ion mobility frame be sliced? Default(-1) assigns all peaks with identical ion-mobility values to a separate spectrum. |
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Split a (TimsTOF) ion mobility frame (i.e. a spectrum concatenated from multiple spectra with different IM values) into separate spectra.
The input im_frame must have a floatDataArray where IM values are annotated. If not, an exception is thrown.
To get some coarser binning, choose a smaller number_of_bins. The default creates a new bin (=spectrum in the output) for each distinct ion mobility value.
| im_frame | Concatenated spectrum representing a frame |
| number_of_bins | In how many bins should the ion mobility frame be sliced? Default(-1) assigns all peaks with identical ion-mobility values to a separate spectrum. |
| Exception::MissingInformation | if im_frame does not have IM data in floatDataArrays |
Referenced by TOPPViewBase::showCurrentPeaksAsIonMobility().
1.9.1