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OpenMS
2.5.0
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#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/ANALYSIS/ID/AccurateMassSearchEngine.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/MzTab.h>
#include <OpenMS/FORMAT/MzTabFile.h>
#include <OpenMS/KERNEL/FeatureMap.h>
EmpiricalFormula parseAdduct_(const String &adduct)
Definition: NucleicAcidSearchEngine.cpp:338
double estimateMedianChromatographicFWHM_(MSExperiment &ms_centroided)
Definition: ProteomicsLFQ.cpp:373
IMType
Definition: FileConverter.cpp:153
void print_usage(Logger::LogStream &stream=OpenMS_Log_info)
Definition: TOPPAS.cpp:100
bool operator()(const NASequence &s)
Definition: NucleicAcidSearchEngine.cpp:334
int main(int argc, const char **argv)
Definition: TOPPAS.cpp:115
PeakSpectrum accumulated
Definition: MetaProSIP.cpp:152
pair< double, vector< double > > IsotopePattern
Definition: MetaProSIP.cpp:85
@ IM_STACKED
ion mobility frame is stacked in a single spectrum
Definition: FileConverter.cpp:156
HasInvalidLength(Size min_size, Size max_size)
Definition: NucleicAcidSearchEngine.cpp:330
int main(int argc, const char **argv)
Definition: Epifany.cpp:364
void collapseIMSpectrum(const MSExperiment &exp, std::vector< MSSpectrum > &result)
Collapses multiple IM spectra from the same frame into a single MSSpectrum.
Definition: FileConverter.cpp:283
multimap< Size, PeptideIdentification > transferIDsBetweenSameFraction_(const ConsensusMap &consensus_fraction, Size min_occurrence=3)
Definition: ProteomicsLFQ.cpp:642
IsotopePatterns patterns
Definition: MetaProSIP.cpp:156
map< String, String > ambiguous_mods_
Definition: NucleicAcidSearchEngine.cpp:155
void link_(vector< FeatureMap > &feature_maps, double median_fwhm, double max_alignment_diff, ConsensusMap &consensus_fraction)
Definition: ProteomicsLFQ.cpp:531
Definition: MetaProSIP.cpp:194
Epifany()
Definition: Epifany.cpp:112
IdentificationData::IdentifiedOligoRef oligo_ref
Definition: NucleicAcidSearchEngine.cpp:273
OpenMS_Architecture getBinaryArchitecture()
Definition: OpenMSInfo.cpp:191
multimap< double, AnnotatedHit, greater< double > > HitsByScore
Definition: NucleicAcidSearchEngine.cpp:280
OpenMS_OS
Definition: OpenMSInfo.cpp:58
Definition: MetaProSIP.cpp:164
bool operator()(const SIPIncorporation &a, const SIPIncorporation &b) const
Definition: MetaProSIP.cpp:187
static Int calculateDecompositionWeightsIsotopicPatterns(Size n_bins, const vector< double > &isotopic_intensities, const IsotopePatterns &patterns, MapRateToScoreType &map_rate_to_decomposition_weight, SIPPeptide &sip_peptide)
> Perform the decomposition
Definition: MetaProSIP.cpp:1256
static bool checkRDependencies(const String &tmp_path, StringList package_names, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:1935
double alignAndLink_(vector< FeatureMap > &feature_maps, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, const double median_fwhm)
Definition: ProteomicsLFQ.cpp:566
map< String, String > mapId2MzMLs_(const map< String, String > &m2i)
Definition: ProteomicsLFQ.cpp:242
void convertPSMScores_(vector< PeptideIdentification > &mergedpeps)
Definition: Epifany.cpp:190
OpenMS_Architecture arch
Definition: OpenMSInfo.cpp:78
void print_usage()
Definition: TOPPView.cpp:84
static IsotopePatterns calculateIsotopePatternsFor18ORangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1780
static vector< double > correlateXICsToMono(const vector< vector< double > > &xics)
Definition: MetaProSIP.cpp:1878
PrecursorInfo(Size scan_index, Int charge, Size isotope, const String &adduct)
Definition: NucleicAcidSearchEngine.cpp:262
You can set more CMake variables adding< code > DVARIABLE
Definition: common-cmake-parameters.doxygen:1
map< double, double > MapRateToScoreType
Definition: MetaProSIP.cpp:84
pair< double, double > checkExtremePSMScores_(vector< PeptideIdentification > &mergedpeps)
Definition: Epifany.cpp:167
Definition: ProteomicsLFQ.cpp:110
static vector< vector< SIPPeptide > > clusterSIPPeptides(const vector< double > ¢ers, vector< SIPPeptide > &sip_peptides)
Definition: MetaProSIP.cpp:320
vector< String > accessions
protein accessions of the peptide
Definition: MetaProSIP.cpp:112
static IsotopePatterns calculateIsotopePatternsFor15NRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1455
void calculateAndFilterFDR_(IdentificationData &id_data, bool only_top_hits)
Definition: NucleicAcidSearchEngine.cpp:841
double mass_theo
uncharged theoretical mass
Definition: MetaProSIP.cpp:118
@ OS_WINDOWS
Definition: OpenMSInfo.cpp:58
Definition: GNPSExport.cpp:79
static IsotopePatterns calculateIsotopePatternsFor13CRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1706
static vector< double > extractXICsOfIsotopeTraces(Size element_count, double mass_diff, double mz_tolerance_ppm, double rt_tolerance_s, double seed_rt, double seed_mz, double seed_charge, const PeakMap &peak_map, const double min_corr_mono=-1.0)
Definition: MetaProSIP.cpp:1891
static vector< vector< double > > extractXICs(double seed_rt, vector< double > xic_mzs, double mz_toelrance_ppm, double rt_tolerance_s, const PeakMap &peak_map)
Definition: MetaProSIP.cpp:1824
map< String, String > mapMzML2Ids_(StringList &in, StringList &in_ids)
Definition: ProteomicsLFQ.cpp:217
Definition: MetaProSIP.cpp:184
static void plotHeatMap(const String &output_dir, const String &tmp_path, const String &file_suffix, const String &file_extension, const vector< vector< double > > &binned_ria, vector< String > class_labels, Size debug_level=0, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:364
@ ARCH_64BIT
Definition: OpenMSInfo.cpp:60
Size max_size_
Definition: NucleicAcidSearchEngine.cpp:328
void processDriftTimeStack(const std::vector< MSSpectrum > &stack, std::vector< MSSpectrum > &result)
Process a stack of drift time spectra.
Definition: FileConverter.cpp:178
void registerOptionsAndFlags_() override
Definition: GNPSExport.cpp:93
@ OS_MACOS
Definition: OpenMSInfo.cpp:58
Size non_zero_decomposition_coefficients
decomposition coefficients significantly larger than 0
Definition: MetaProSIP.cpp:146
Definition: NucleicAcidSearchEngine.cpp:140
String getArchAsString() const
Definition: OpenMSInfo.cpp:85
double feature_rt
measurement time of feature apex [s]
Definition: MetaProSIP.cpp:122
const char * tool_name
Definition: TOPPView.cpp:78
void transform_(vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations)
Definition: ProteomicsLFQ.cpp:499
NucleicAcidSearchEngine()
Definition: NucleicAcidSearchEngine.cpp:146
ExitCodes quantifyFraction_(const pair< unsigned int, std::vector< String > > &ms_files, const map< String, String > &mzfile2idfile, double median_fwhm, const multimap< Size, PeptideIdentification > &transfered_ids, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, double &max_alignment_diff, set< String > &fixed_modifications, set< String > &variable_modifications)
Definition: ProteomicsLFQ.cpp:696
double mz_theo
theoretical mz
Definition: MetaProSIP.cpp:116
String os_version
Definition: OpenMSInfo.cpp:77
void postProcessHits_(const PeakMap &exp, vector< HitsByScore > &annotated_hits, IdentificationData &id_data, bool negative_mode)
Definition: NucleicAcidSearchEngine.cpp:738
void removeExtremeValues_(vector< PeptideIdentification > &mergedpeps, double minscore, double maxscore)
Definition: Epifany.cpp:222
static void createQualityReport(const String &tmp_path, const String &qc_output_directory, const String &file_suffix, const String &file_extension, const vector< vector< SIPPeptide > > &sip_peptide_cluster, Size n_heatmap_bins, double score_plot_y_axis_min, bool report_natural_peptides, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:766
double abundance
abundance of isotopologue
Definition: MetaProSIP.cpp:101
bool resolve_ambiguous_mods_
Definition: NucleicAcidSearchEngine.cpp:156
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
@ OS_LINUX
Definition: OpenMSInfo.cpp:58
ExitCodes main_(int, const char **) override
Definition: Epifany.cpp:235
Definition: MetaProSIP.cpp:265
bool unique
if the peptide is unique and therefor identifies the protein umambigously
Definition: MetaProSIP.cpp:114
double global_LR
labeling ratio for the whole spectrum used to detect global drifts. 13C/(12C+13C) intensities....
Definition: MetaProSIP.cpp:132
PeakSpectrum reconstruction
signal reconstruction (debugging)
Definition: MetaProSIP.cpp:148
@ ARCH_UNKNOWN
Definition: OpenMSInfo.cpp:60
String extractCachedMetaFilename(const String &in)
Definition: FileConverter.cpp:136
vector< IsotopePattern > IsotopePatterns
Definition: MetaProSIP.cpp:86
static void createPeptideCentricCSVReport(const String &in_mzML, const String &file_extension, vector< vector< SIPPeptide > > &sippeptide_cluster, ofstream &os, map< String, String > &proteinid_to_description, String qc_output_directory, String file_suffix, bool report_natural_peptides)
Definition: MetaProSIP.cpp:1102
IMType determineIMType(const MSExperiment &exp)
Definition: FileConverter.cpp:160
MapRateToScoreType correlation_map
Definition: MetaProSIP.cpp:138
void preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool negative_mode, Int min_charge, Int max_charge, bool include_unknown_charge)
Definition: NucleicAcidSearchEngine.cpp:531
static vector< double > getRIAClusterCenter(const vector< SIPPeptide > &sip_peptides, bool debug=false)
Definition: MetaProSIP.cpp:268
double score
search engine score or q-value if fdr filtering is applied
Definition: MetaProSIP.cpp:120
Definition: MetaProSIP.cpp:1252
String adduct
Definition: NucleicAcidSearchEngine.cpp:260
You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > this flag can be used to disable those parts of the documentation and the tests that need an X Server(Default:On)</td ></tr >< tr >< td valign
vector< double > reconstruction_monoistopic
signal reconstruction of natural peptide (at mono-isotopic peak)
Definition: MetaProSIP.cpp:150
double explained_TIC_fraction
fraction of the MS2 TIC that is explained by the maximum correlating decomposition weights
Definition: MetaProSIP.cpp:142
ExitCodes main_(int, const char **) override
Definition: GNPSExport.cpp:115
Size scan_index
Definition: NucleicAcidSearchEngine.cpp:257
static IsotopePatterns calculateIsotopePatternsFor18ORange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1595
void recalibrateMasses_(MSExperiment &ms_centroided, vector< PeptideIdentification > &peptide_ids, const String &id_file_abs_path)
Definition: ProteomicsLFQ.cpp:328
void registerOptionsAndFlags_() override
Definition: ProteomicsLFQ.cpp:120
@ ARCH_32BIT
Definition: OpenMSInfo.cpp:60
int main(int argc, const char **argv)
Definition: NucleicAcidSearchEngine.cpp:1378
NASequence sequence
Definition: NucleicAcidSearchEngine.cpp:274
Definition: INIFileEditorWindow.cpp:52
double calculatePrecursorMass_(double mz, Int charge, Int isotope, double adduct_mass, bool negative_mode)
Definition: NucleicAcidSearchEngine.cpp:656
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
const PrecursorInfo * precursor_ref
Definition: NucleicAcidSearchEngine.cpp:277
void registerOptionsAndFlags_()
Definition: NucleicAcidSearchEngine.cpp:159
void resolveAmbiguousMods_(HitsByScore &hits)
Definition: NucleicAcidSearchEngine.cpp:677
static vector< RateScorePair > getHighPoints(double threshold, const MapRateToScoreType &rate2score, bool debug=false)
< Determine score maxima from rate to score distribution using derivatives from spline interpolation
Definition: MetaProSIP.cpp:198
UTILProteomicsLFQ()
Definition: ProteomicsLFQ.cpp:114
void registerOptionsAndFlags_() override
Definition: Epifany.cpp:119
int main(int argc, const char **argv)
Definition: TOPPView.cpp:108
std::string OpenMS_OSNames[]
Definition: OpenMSInfo.cpp:59
vector< String > fragment_ion_codes_
Definition: NucleicAcidSearchEngine.cpp:154
void generateLFQInput_(IdentificationData &id_data, const String &out_file)
Definition: NucleicAcidSearchEngine.cpp:869
static IsotopePatterns calculateIsotopePatternsFor2HRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1742
Definition: OpenMSInfo.cpp:68
Param getSubsectionDefaults_(const String &) const override
Definition: Epifany.cpp:162
Definition: NucleicAcidSearchEngine.cpp:255
void registerIDMetaData_(IdentificationData &id_data, const String &in_mzml, const vector< String > &primary_files, const IdentificationData::DBSearchParam &search_param)
Definition: NucleicAcidSearchEngine.cpp:807
double align_(vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations)
Definition: ProteomicsLFQ.cpp:432
OpenMSOSInfo()
Definition: OpenMSInfo.cpp:70
double precursor_error_ppm
Definition: NucleicAcidSearchEngine.cpp:275
vector< PeptideHit::PeakAnnotation > annotations
Definition: NucleicAcidSearchEngine.cpp:276
void calculateSeeds_(const MSExperiment &ms_centroided, FeatureMap &seeds, double median_fwhm)
Definition: ProteomicsLFQ.cpp:399
set< ConstRibonucleotidePtr > getModifications_(const set< String > &mod_names)
Definition: NucleicAcidSearchEngine.cpp:283
int main(int argc, const char **argv)
Definition: ProteomicsLFQ.cpp:1622
static Size getNumberOfLabelingElements(const String &labeling_element, const AASequence &peptide)
Definition: MetaProSIP.cpp:1409
Size isotope
Definition: NucleicAcidSearchEngine.cpp:259
double mass_diff
Definition: MetaProSIP.cpp:130
double correlation
correlation coefficient
Definition: MetaProSIP.cpp:99
Definition: MetaProSIP.cpp:1931
Definition: OpenMSInfo.cpp:55
Definition: MetaProSIP.cpp:361
static OpenMSOSInfo getOSInfo()
Definition: OpenMSInfo.cpp:92
Int charge
Definition: NucleicAcidSearchEngine.cpp:258
@ IM_NONE
no ion mobility
Definition: FileConverter.cpp:155
Definition: NucleicAcidSearchEngine.cpp:325
OpenMS_Architecture
Definition: OpenMSInfo.cpp:60
ExitCodes centroidAndCorrectPrecursors_(const String &mz_file, MSExperiment &ms_centroided)
Definition: ProteomicsLFQ.cpp:252
vector< SIPIncorporation > incorporations
Definition: MetaProSIP.cpp:154
datastructure for reporting a peptide with one or more incorporation rates
Definition: MetaProSIP.cpp:108
Definition: MetaProSIP.cpp:174
Definition: MetaProSIP.cpp:88
datastructure for reporting an incorporation event
Definition: MetaProSIP.cpp:95
const Ribonucleotide * ConstRibonucleotidePtr
Definition: NucleicAcidSearchEngine.cpp:143
ExitCodes main_(int, const char **) override
Definition: ProteomicsLFQ.cpp:1007
void deisotopeAndSingleChargeMSSpectrum_(MSSpectrum &in, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_unit_ppm, bool keep_only_deisotoped=false, Size min_isopeaks=3, Size max_isopeaks=10, bool make_single_charged=true)
Definition: NucleicAcidSearchEngine.cpp:375
OpenMS_OS os
Definition: OpenMSInfo.cpp:76
String feature_type
used to distinguish features from FeatureFinder, or synthetised from ids or averagine ids in reportin...
Definition: MetaProSIP.cpp:144
bool operator()(const pair< SIPPeptide, Size > &a, const pair< SIPPeptide, Size > &b) const
Definition: MetaProSIP.cpp:177
AASequence sequence
sequence of the peptide
Definition: MetaProSIP.cpp:110
void expandIMSpectrum(const MSSpectrum &tmps, std::vector< MSSpectrum > &result)
Expands a single MSSpectrum (single frame) into individual ion mobility spectrum.
Definition: FileConverter.cpp:226
@ OS_UNKNOWN
Definition: OpenMSInfo.cpp:58
const char * tool_name
Definition: TOPPAS.cpp:94
static void plotFilteredSpectra(const String &output_dir, const String &tmp_path, const String &file_suffix, const String &file_extension, const vector< SIPPeptide > &sip_peptides, Size debug_level=0, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:467
static IsotopePatterns calculateIsotopePatternsFor2HRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1524
Definition: MetaProSIP.cpp:1821
double RR
R squared of NNLS fit.
Definition: MetaProSIP.cpp:140
You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > DCMAKE_PREFIX_PATH
Definition: common-cmake-parameters.doxygen:19
Definition: Epifany.cpp:108
static void createCSVReport(vector< vector< SIPPeptide > > &sippeptide_cluster, ofstream &os, map< String, String > &proteinid_to_description)
Definition: MetaProSIP.cpp:809
static void writeHTML(const String &qc_output_directory, const String &file_suffix, const String &file_extension, const vector< SIPPeptide > &sip_peptides)
Definition: MetaProSIP.cpp:545
Int charge
charge of the peptide feature
Definition: MetaProSIP.cpp:128
double feature_mz
mz of feature apex [s]
Definition: MetaProSIP.cpp:124
String getOSAsString() const
Definition: OpenMSInfo.cpp:80
ExitCodes main_(int, const char **) override
Definition: NucleicAcidSearchEngine.cpp:922
vector< RateScorePair > correlation_maxima
Definition: MetaProSIP.cpp:134
Definition: NucleicAcidSearchEngine.cpp:271
#define SEP
Definition: DigestorMotif.cpp:49
map< pair< String, UInt >, vector< int > > getPeptideOccurrence_(const ConsensusMap &cons)
Definition: ProteomicsLFQ.cpp:601
std::string OpenMS_ArchNames[]
Definition: OpenMSInfo.cpp:61
static IsotopePatterns calculateIsotopePatternsFor13CRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1336
@ IM_MULTIPLE_SPECTRA
ion mobility is recorded as multiple spectra per frame
Definition: FileConverter.cpp:157
static void createBinnedPeptideRIAData_(const Size n_heatmap_bins, const vector< vector< SIPPeptide > > &sip_clusters, vector< vector< double > > &binned_peptide_ria, vector< String > &cluster_labels)
Definition: MetaProSIP.cpp:1226
double rate
rate
Definition: MetaProSIP.cpp:97
int main(int argc, const char **argv)
Definition: GNPSExport.cpp:378
static void plotScoresAndWeights(const String &output_dir, const String &tmp_path, const String &file_suffix, const String &file_extension, const vector< SIPPeptide > &sip_peptides, double score_plot_yaxis_min, Size debug_level=0, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:666
bool operator()(const vector< SIPPeptide > &a, const vector< SIPPeptide > &b) const
Definition: MetaProSIP.cpp:167
TOPPGNPSExport()
Definition: GNPSExport.cpp:82
MapRateToScoreType decomposition_map
Definition: MetaProSIP.cpp:136
static IsotopePatterns calculateIsotopePatternsFor15NRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1667
Size min_size_
Definition: NucleicAcidSearchEngine.cpp:327