Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
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com.compomics.util.experiment.quantification.reporterion |
Experiment classes related to reporter ions.
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Modifier and Type | Method and Description |
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ArrayList<ReporterIon> |
PTM.getReporterIons()
Returns the reporter ions possibly encountered with this modification.
|
Modifier and Type | Method and Description |
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void |
PTM.addReporterIon(ReporterIon reporterIon)
Adds a reporter ion.
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Modifier and Type | Method and Description |
---|---|
void |
PTM.setReporterIons(ArrayList<ReporterIon> reporterIons)
Sets the reporter ions possibly encountered with this modification.
|
Modifier and Type | Field and Description |
---|---|
static ReporterIon |
ReporterIon.ACE_K_126
Standard reporter ion for lysine acetylation (PMID: 18338905).
|
static ReporterIon |
ReporterIon.ACE_K_143
Standard reporter ion for lysine acetylation (PMID: 18338905).
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static ReporterIon |
ReporterIon.DI_METHYL_R_112
Standard reporter ion for di-methylation of R (PMID: 16335983).
|
static ReporterIon |
ReporterIon.DI_METHYL_R_115
Standard reporter ion for di-methylation of R (PMID: 16335983).
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static ReporterIon |
ReporterIon.DI_METHYL_R_157
Standard reporter ion for di-methylation of R (PMID: 16335983).
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static ReporterIon |
ReporterIon.FORMYL_K
Standard reporter ion for formylation of K (PMID: 24895383).
|
static ReporterIon |
ReporterIon.iTRAQ_145
Standard reporter ion iTRAQ (reporter + balancer).
|
static ReporterIon |
ReporterIon.iTRAQ_305
Standard reporter ion iTRAQ (reporter + balancer).
|
static ReporterIon |
ReporterIon.iTRAQ4Plex_114
Standard reporter ion iTRAQ 4Plex 114.
|
static ReporterIon |
ReporterIon.iTRAQ4Plex_115
Standard reporter ion iTRAQ 4Plex 115.
|
static ReporterIon |
ReporterIon.iTRAQ4Plex_116
Standard reporter ion iTRAQ 4Plex 116.
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static ReporterIon |
ReporterIon.iTRAQ4Plex_117
Standard reporter ion iTRAQ 4Plex 117.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_113
Standard reporter ion iTRAQ 8Plex 113.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_114
Standard reporter ion iTRAQ 8Plex 114.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_115
Standard reporter ion iTRAQ 8Plex 115.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_116
Standard reporter ion iTRAQ 8Plex 116.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_117
Standard reporter ion iTRAQ 8Plex 117.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_118
Standard reporter ion iTRAQ 8Plex 118.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_119
Standard reporter ion iTRAQ 8Plex 119.
|
static ReporterIon |
ReporterIon.iTRAQ8Plex_121
Standard reporter ion iTRAQ 8Plex 121.
|
static ReporterIon |
ReporterIon.METHYL_R_112
Standard reporter ion for methylation of R (PMID: 16335983).
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static ReporterIon |
ReporterIon.METHYL_R_115
Standard reporter ion for methylation of R (PMID: 16335983).
|
static ReporterIon |
ReporterIon.METHYL_R_143
Standard reporter ion for methylation of R (PMID: 16335983).
|
static ReporterIon |
ReporterIon.METHYL_R_70
Standard reporter ion for methylation of R (PMID: 16335983).
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static ReporterIon |
ReporterIon.METHYL_R_87
Standard reporter ion for methylation of R.
|
static ReporterIon |
ReporterIon.PHOSPHO_Y
Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).
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static ReporterIon |
ReporterIon.QQ
Standard reporter ion for SUMO-2/3 Q87R.
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static ReporterIon |
ReporterIon.QQ_H2O
Standard reporter ion for SUMO-2/3 Q87R.
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static ReporterIon |
ReporterIon.QQT
Standard reporter ion for SUMO-2/3 Q87R.
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static ReporterIon |
ReporterIon.QQT_H2O
Standard reporter ion for SUMO-2/3 Q87R.
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static ReporterIon |
ReporterIon.QQTG
Standard reporter ion for SUMO-2/3 Q87R.
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static ReporterIon |
ReporterIon.QQTG_H2O
Standard reporter ion for SUMO-2/3 Q87R.
|
static ReporterIon |
ReporterIon.QQTGG
Standard reporter ion for SUMO-2/3 Q87R.
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static ReporterIon |
ReporterIon.QQTGG_H2O
Standard reporter ion for SUMO-2/3 Q87R.
|
static ReporterIon |
ReporterIon.TMT_126
Standard reporter ion TMT 126.
|
static ReporterIon |
ReporterIon.TMT_126_ETD
Standard reporter ion TMT 126 with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_127C
Standard reporter ion TMT 127C.
|
static ReporterIon |
ReporterIon.TMT_127C_ETD
Standard reporter ion TMT 127C with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_127N
Standard reporter ion TMT 127N.
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static ReporterIon |
ReporterIon.TMT_127N_ETD
Standard reporter ion TMT 127N with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_128C
Standard reporter ion TMT 128C.
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static ReporterIon |
ReporterIon.TMT_128C_ETD
Standard reporter ion TMT 128C with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_128N
Standard reporter ion TMT 128N.
|
static ReporterIon |
ReporterIon.TMT_128N_ETD
Standard reporter ion TMT 128N with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_129C
Standard reporter ion TMT 129C.
|
static ReporterIon |
ReporterIon.TMT_129C_ETD
Standard reporter ion TMT 129C with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_129N
Standard reporter ion TMT 129N.
|
static ReporterIon |
ReporterIon.TMT_129N_ETD
Standard reporter ion TMT 129N with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_130C
Standard reporter ion TMT 130C.
|
static ReporterIon |
ReporterIon.TMT_130C_ETD
Standard reporter ion TMT 130C with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_130N
Standard reporter ion TMT 130N.
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static ReporterIon |
ReporterIon.TMT_130N_ETD
Standard reporter ion TMT 130N with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_131
Standard reporter ion TMT 131.
|
static ReporterIon |
ReporterIon.TMT_131_ETD
Standard reporter ion TMT 131 with ETD fragmentation.
|
static ReporterIon |
ReporterIon.TMT_226
Standard reporter ion TMT (reporter + balancer).
|
static ReporterIon |
ReporterIon.TMT_230
Standard reporter ion TMT (reporter + balancer).
|
Modifier and Type | Method and Description |
---|---|
ReporterIon |
ReporterIon.clone() |
static ReporterIon |
ReporterIon.getReporterIon(int subType)
Returns the reporter ion indexed by the given index.
|
static ReporterIon |
ReporterIon.getReporterIon(String name)
Returns the reporter ion corresponding to the given name.
|
Modifier and Type | Method and Description |
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static void |
ReporterIon.addReporterIon(ReporterIon reporterIon)
Adds a reporter ion to the class static map.
|
boolean |
ReporterIon.isSameAs(ReporterIon anotherReporterIon)
Compares the current reporter ion with another one based on their masses.
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Modifier and Type | Method and Description |
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ReporterIon |
Reagent.getReporterIon()
Returns the reporter ion to look for in the spectrum.
|
ReporterIon |
ReporterMethod.getReporterIon(String reporterIonName)
Returns the reporter ion of the given name, null if not found.
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Modifier and Type | Method and Description |
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void |
Reagent.setReporterIon(ReporterIon reporterIon)
Sets the reporter ion to look for in the spectrum.
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