Package | Description |
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.biology.ions |
This package contains experiment classes related to ions.
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com.compomics.util.experiment.quantification.reporterion |
This package contains 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 |
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void |
PTM.setReporterIons(ArrayList<ReporterIon> reporterIons)
Sets the reporter ions possibly encountered with this modification.
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Modifier and Type | Field and Description |
---|---|
static ReporterIon |
ReporterIon.ACE_K_126
Standard reporter ion for lysine acetylation (PMID: 18338905).
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static ReporterIon |
ReporterIon.ACE_K_143
Standard reporter ion for lysine acetylation (PMID: 18338905).
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static ReporterIon |
ReporterIon.iTRAQ_145
Standard reporter ion iTRAQ (reporter + balancer).
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static ReporterIon |
ReporterIon.iTRAQ_305
Standard reporter ion iTRAQ (reporter + balancer).
|
static ReporterIon |
ReporterIon.iTRAQ113
Standard reporter ion iTRAQ 113.
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static ReporterIon |
ReporterIon.iTRAQ114
Standard reporter ion iTRAQ 114.
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static ReporterIon |
ReporterIon.iTRAQ115
Standard reporter ion iTRAQ 115.
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static ReporterIon |
ReporterIon.iTRAQ116
Standard reporter ion iTRAQ 116.
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static ReporterIon |
ReporterIon.iTRAQ117
Standard reporter ion iTRAQ 117.
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static ReporterIon |
ReporterIon.iTRAQ118
Standard reporter ion iTRAQ 118.
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static ReporterIon |
ReporterIon.iTRAQ119
Standard reporter ion iTRAQ 119.
|
static ReporterIon |
ReporterIon.iTRAQ121
Standard reporter ion iTRAQ 121.
|
static ReporterIon |
ReporterIon.PHOSPHO_Y
Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).
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static ReporterIon |
ReporterIon.TMT_226
Standard reporter ion TMT (reporter + balancer).
|
static ReporterIon |
ReporterIon.TMT_230
Standard reporter ion TMT (reporter + balancer).
|
static ReporterIon |
ReporterIon.TMT126
Standard reporter ion TMT0.
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static ReporterIon |
ReporterIon.TMT127
Standard reporter ion TMT1.
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static ReporterIon |
ReporterIon.TMT128
Standard reporter ion TMT2.
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static ReporterIon |
ReporterIon.TMT129
Standard reporter ion TMT3.
|
static ReporterIon |
ReporterIon.TMT130
Standard reporter ion TMT4.
|
static ReporterIon |
ReporterIon.TMT131
Standard reporter ion TMT5.
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Modifier and Type | Method and Description |
---|---|
static ReporterIon |
ReporterIon.getReporterIon(int subType)
Returns the reporter ion indexed by the given index.
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static ReporterIon |
ReporterIon.getReporterIon(String name)
Returns the reporter ion corresponding to the given name.
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Modifier and Type | Method and Description |
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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 |
---|---|
void |
Reagent.setReporterIon(ReporterIon reporterIon)
Sets the reporter ion to look for in the spectrum.
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