35 #ifndef OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H
36 #define OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H
42 #include <gsl/gsl_interp.h>
43 #include <gsl/gsl_spline.h>
190 bool intensityFilter_();
224 std::vector<DoubleReal> getPeakPositions();
229 const std::vector<DoubleReal> & getExpectedMzShifts();
234 std::vector<SILACPattern> & getElements();
244 std::vector<DoubleReal> & getMassSeparations();
Size isotopes_per_peptide_
number of peaks per peptide to search for
Definition: SILACFilter.h:83
DoubleReal model_deviation_
maximal value of which a predicted SILAC feature may deviate from the averagine model ...
Definition: SILACFilter.h:78
static IsotopeDistributionCache * isotope_distribution_
Definition: SILACFilter.h:103
std::vector< std::vector< DoubleReal > > exact_shifts_
exact m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the light ...
Definition: SILACFilter.h:143
DoubleReal intensity_cutoff_
minimal intensity of SILAC features
Definition: SILACFilter.h:88
DoubleReal isotope_distance_
distance between isotopic peaks of a peptide in [Th]
Definition: SILACFilter.h:128
Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:277
Filter to use for SILACFiltering.
Definition: SILACFilter.h:58
bool allow_missing_peaks_
flag for missing peaks
Definition: SILACFilter.h:98
std::vector< DoubleReal > mass_separations_
mass shift(s) in [Da] to search for
Definition: SILACFilter.h:68
std::vector< SILACPattern > elements_
holds the recognized features
Definition: SILACFilter.h:133
Size number_of_peptides_
number of peptides [i.e. number of labelled peptides +1, e.g. for SILAC triplet =3] ...
Definition: SILACFilter.h:108
DoubleReal current_mz_
m/z at which the filter is currently applied to
Definition: SILACFilter.h:138
std::vector< DoubleReal > peak_positions_
peak positions of SILAC pattern
Definition: SILACFilter.h:113
std::vector< std::vector< DoubleReal > > exact_mz_positions_
m/z positions mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of ...
Definition: SILACFilter.h:148
Wrapper class for spectrum interpolation.
Definition: SILACFiltering.h:76
std::vector< DoubleReal > expected_mz_shifts_
m/z shifts relative to mono-isotopic peak of unlabelled peptide
Definition: SILACFilter.h:123
std::vector< std::vector< DoubleReal > > exact_intensities_
intensities at mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of...
Definition: SILACFilter.h:153
DoubleReal intensity_correlation_
minimal intensity correlation between regions of different peaks
Definition: SILACFilter.h:93
Int charge_
charge of the ions to search for
Definition: SILACFilter.h:73
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
IsotopeDistributionCache::TheoreticalIsotopePattern TheoreticalIsotopePattern
Definition: SILACFilter.h:63
A single SILAC pattern containing multiple found points.
Definition: SILACPattern.h:47
std::vector< DoubleReal > mz_peptide_separations_
m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}]
Definition: SILACFilter.h:118
Prealculate isotope distributions for interesting mass ranges.
Definition: IsotopeDistributionCache.h:46
int Int
Signed integer type.
Definition: Types.h:100
std::vector< std::vector< DoubleReal > > expected_shifts_
expected m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the lig...
Definition: SILACFilter.h:158
Filtering for SILAC data.
Definition: SILACFiltering.h:62