Uses of Class
com.compomics.util.experiment.biology.ions.impl.ReporterIon
Packages that use ReporterIon
Package
Description
Ion implementations.
This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
Experiment classes related to reporter ions.
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Uses of ReporterIon in com.compomics.util.experiment.biology.ions.impl
Fields in com.compomics.util.experiment.biology.ions.impl declared as ReporterIonModifier and TypeFieldDescriptionstatic final ReporterIonReporterIon.ACE_K_126Standard reporter ion for lysine acetylation (PMID: 18338905).static final ReporterIonReporterIon.ACE_K_143Standard reporter ion for lysine acetylation (PMID: 18338905).static final ReporterIonReporterIon.DI_METHYL_R_112Standard reporter ion for di-methylation of R (PMID: 16335983).static final ReporterIonReporterIon.DI_METHYL_R_115Standard reporter ion for di-methylation of R (PMID: 16335983).static final ReporterIonReporterIon.DI_METHYL_R_157Standard reporter ion for di-methylation of R (PMID: 16335983).static final ReporterIonReporterIon.FORMYL_KStandard reporter ion for formylation of K (PMID: 24895383).static final ReporterIonReporterIon.iodoTMT_126Standard reporter ion iodoTMT 126.static final ReporterIonReporterIon.iodoTMT_126_ETDStandard reporter ion iodoTMT 126 with ETD fragmentation.static final ReporterIonReporterIon.iodoTMT_127Standard reporter ion iodoTMT 127.static final ReporterIonReporterIon.iodoTMT_127_ETDStandard reporter ion iodoTMT 127 with ETD fragmentation.static final ReporterIonReporterIon.iodoTMT_128Standard reporter ion iodoTMT 128.static final ReporterIonReporterIon.iodoTMT_128_ETDStandard reporter ion iodoTMT 128 with ETD fragmentation.static final ReporterIonReporterIon.iodoTMT_129Standard reporter ion iodoTMT 128.static final ReporterIonReporterIon.iodoTMT_129_ETDStandard reporter ion iodoTMT 128 with ETD fragmentation.static final ReporterIonReporterIon.iodoTMT_130Standard reporter ion iodoTMT 130.static final ReporterIonReporterIon.iodoTMT_130_ETDStandard reporter ion iodoTMT 130 with ETD fragmentation.static final ReporterIonReporterIon.iodoTMT_131Standard reporter ion iodoTMT 131.static final ReporterIonReporterIon.iodoTMT_131_ETDStandard reporter ion iodoTMT 131 with ETD fragmentation.static final ReporterIonReporterIon.iodoTMT_zeroStandard reporter ion iodoTMT zero.static final ReporterIonReporterIon.iodoTMT_zero_ETDStandard reporter ion iodoTMT zero with ETD fragmentation.static final ReporterIonReporterIon.iTRAQ_145Standard reporter ion iTRAQ (reporter + balancer).static final ReporterIonReporterIon.iTRAQ_305Standard reporter ion iTRAQ (reporter + balancer).static final ReporterIonReporterIon.iTRAQ4Plex_114Standard reporter ion iTRAQ 4Plex 114.static final ReporterIonReporterIon.iTRAQ4Plex_115Standard reporter ion iTRAQ 4Plex 115.static final ReporterIonReporterIon.iTRAQ4Plex_116Standard reporter ion iTRAQ 4Plex 116.static final ReporterIonReporterIon.iTRAQ4Plex_117Standard reporter ion iTRAQ 4Plex 117.static final ReporterIonReporterIon.iTRAQ8Plex_113Standard reporter ion iTRAQ 8Plex 113.static final ReporterIonReporterIon.iTRAQ8Plex_114Standard reporter ion iTRAQ 8Plex 114.static final ReporterIonReporterIon.iTRAQ8Plex_115Standard reporter ion iTRAQ 8Plex 115.static final ReporterIonReporterIon.iTRAQ8Plex_116Standard reporter ion iTRAQ 8Plex 116.static final ReporterIonReporterIon.iTRAQ8Plex_117Standard reporter ion iTRAQ 8Plex 117.static final ReporterIonReporterIon.iTRAQ8Plex_118Standard reporter ion iTRAQ 8Plex 118.static final ReporterIonReporterIon.iTRAQ8Plex_119Standard reporter ion iTRAQ 8Plex 119.static final ReporterIonReporterIon.iTRAQ8Plex_121Standard reporter ion iTRAQ 8Plex 121.static final ReporterIonReporterIon.METHYL_R_112Standard reporter ion for methylation of R (PMID: 16335983).static final ReporterIonReporterIon.METHYL_R_115Standard reporter ion for methylation of R (PMID: 16335983).static final ReporterIonReporterIon.METHYL_R_143Standard reporter ion for methylation of R (PMID: 16335983).static final ReporterIonReporterIon.METHYL_R_70Standard reporter ion for methylation of R (PMID: 16335983).static final ReporterIonReporterIon.METHYL_R_87Standard reporter ion for methylation of R.static final ReporterIonReporterIon.PHOSPHO_YStandard reporter ion for phosphorylation of tyrosine (PMID: 11473401).static final ReporterIonReporterIon.QQStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.QQ_H2OStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.QQTStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.QQT_H2OStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.QQTGStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.QQTG_H2OStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.QQTGGStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.QQTGG_H2OStandard reporter ion for SUMO-2/3 Q87R.static final ReporterIonReporterIon.TMT_126Standard reporter ion TMT 126.static final ReporterIonReporterIon.TMT_126_ETDStandard reporter ion TMT 126 with ETD fragmentation.static final ReporterIonReporterIon.TMT_127CStandard reporter ion TMT 127C.static final ReporterIonReporterIon.TMT_127C_ETDStandard reporter ion TMT 127C with ETD fragmentation.static final ReporterIonReporterIon.TMT_127NStandard reporter ion TMT 127N.static final ReporterIonReporterIon.TMT_127N_ETDStandard reporter ion TMT 127N with ETD fragmentation.static final ReporterIonReporterIon.TMT_128CStandard reporter ion TMT 128C.static final ReporterIonReporterIon.TMT_128C_ETDStandard reporter ion TMT 128C with ETD fragmentation.static final ReporterIonReporterIon.TMT_128NStandard reporter ion TMT 128N.static final ReporterIonReporterIon.TMT_128N_ETDStandard reporter ion TMT 128N with ETD fragmentation.static final ReporterIonReporterIon.TMT_129CStandard reporter ion TMT 129C.static final ReporterIonReporterIon.TMT_129C_ETDStandard reporter ion TMT 129C with ETD fragmentation.static final ReporterIonReporterIon.TMT_129NStandard reporter ion TMT 129N.static final ReporterIonReporterIon.TMT_129N_ETDStandard reporter ion TMT 129N with ETD fragmentation.static final ReporterIonReporterIon.TMT_130CStandard reporter ion TMT 130C.static final ReporterIonReporterIon.TMT_130C_ETDStandard reporter ion TMT 130C with ETD fragmentation.static final ReporterIonReporterIon.TMT_130NStandard reporter ion TMT 130N.static final ReporterIonReporterIon.TMT_130N_ETDStandard reporter ion TMT 130N with ETD fragmentation.static final ReporterIonReporterIon.TMT_131Standard reporter ion TMT 131.static final ReporterIonReporterIon.TMT_131_ETDStandard reporter ion TMT 131 with ETD fragmentation.static final ReporterIonReporterIon.TMT_131CStandard reporter ion TMT 131C.static final ReporterIonReporterIon.TMT_131C_ETDStandard reporter ion TMT 131C with ETD fragmentation.static final ReporterIonReporterIon.TMT_226Standard reporter ion TMT (reporter + balancer).static final ReporterIonReporterIon.TMT_230Standard reporter ion TMT (reporter + balancer).static final ReporterIonReporterIon.TMTpro_126Standard reporter ion TMTpro-126.static final ReporterIonReporterIon.TMTpro_127CStandard reporter ion TMTpro-127C.static final ReporterIonReporterIon.TMTpro_127NStandard reporter ion TMTpro-127N.static final ReporterIonReporterIon.TMTpro_128CStandard reporter ion TMTpro-128C.static final ReporterIonReporterIon.TMTpro_128NStandard reporter ion TMTpro-128N.static final ReporterIonReporterIon.TMTpro_129CStandard reporter ion TMTpro-129C.static final ReporterIonReporterIon.TMTpro_129NStandard reporter ion TMTpro-129N.static final ReporterIonReporterIon.TMTpro_130CStandard reporter ion TMTpro-130C.static final ReporterIonReporterIon.TMTpro_130NStandard reporter ion TMTpro-130N.static final ReporterIonReporterIon.TMTpro_131CStandard reporter ion TMTpro-131C.static final ReporterIonReporterIon.TMTpro_131NStandard reporter ion TMTpro-131N.static final ReporterIonReporterIon.TMTpro_132CStandard reporter ion TMTpro-132C.static final ReporterIonReporterIon.TMTpro_132NStandard reporter ion TMTpro-132N.static final ReporterIonReporterIon.TMTpro_133CStandard reporter ion TMTpro-133C.static final ReporterIonReporterIon.TMTpro_133NStandard reporter ion TMTpro-133N.static final ReporterIonReporterIon.TMTpro_134CStandard reporter ion TMTpro-134C.static final ReporterIonReporterIon.TMTpro_134NStandard reporter ion TMTpro-134N.static final ReporterIonReporterIon.TMTpro_135NStandard reporter ion TMTpro-135N.Methods in com.compomics.util.experiment.biology.ions.impl that return ReporterIonModifier and TypeMethodDescriptionReporterIon.clone()static ReporterIonReporterIon.getReporterIon(int subType) Returns the reporter ion indexed by the given index.static ReporterIonReporterIon.getReporterIon(String name) Returns the reporter ion corresponding to the given name.Methods in com.compomics.util.experiment.biology.ions.impl with parameters of type ReporterIonModifier and TypeMethodDescriptionstatic voidReporterIon.addReporterIon(ReporterIon reporterIon) Adds a reporter ion to the class static map.booleanReporterIon.isSameAs(ReporterIon anotherReporterIon) Compares the current reporter ion with another one based on their masses. -
Uses of ReporterIon in com.compomics.util.experiment.biology.modifications
Methods in com.compomics.util.experiment.biology.modifications that return types with arguments of type ReporterIonModifier and TypeMethodDescriptionModification.getReporterIons()Returns the reporter ions possibly encountered with this modification.Methods in com.compomics.util.experiment.biology.modifications with parameters of type ReporterIonModifier and TypeMethodDescriptionvoidModification.addReporterIon(ReporterIon reporterIon) Adds a reporter ion.Method parameters in com.compomics.util.experiment.biology.modifications with type arguments of type ReporterIonModifier and TypeMethodDescriptionvoidModification.setReporterIons(ArrayList<ReporterIon> reporterIons) Sets the reporter ions possibly encountered with this modification. -
Uses of ReporterIon in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
Constructors in com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators with parameters of type ReporterIon -
Uses of ReporterIon in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
Constructors in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type ReporterIonModifierConstructorDescriptionSimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, boolean a, boolean b, boolean c, boolean x, boolean y, boolean z, boolean precursor, boolean immonium, boolean related, boolean reporter, boolean neutralLosses, boolean neutralLossesSequenceDependent, ReporterIon[] reporterIons) Constructor. -
Uses of ReporterIon in com.compomics.util.experiment.quantification.reporterion
Methods in com.compomics.util.experiment.quantification.reporterion that return ReporterIonModifier and TypeMethodDescriptionReagent.getReporterIon()Returns the reporter ion to look for in the spectrum.ReporterMethod.getReporterIon(String reporterIonName) Returns the reporter ion of the given name, null if not found.Methods in com.compomics.util.experiment.quantification.reporterion with parameters of type ReporterIonModifier and TypeMethodDescriptionvoidReagent.setReporterIon(ReporterIon reporterIon) Sets the reporter ion to look for in the spectrum.