Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
|
com.compomics.util.experiment.quantification.reporterion |
Experiment classes related to reporter ions.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<ReporterIon> |
PTM.getReporterIons()
Returns the reporter ions possibly encountered with this modification.
|
Modifier and Type | Method and Description |
---|---|
void |
PTM.addReporterIon(ReporterIon reporterIon)
Adds a reporter ion.
|
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).
|
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.iTRAQ113
Standard reporter ion iTRAQ 113.
|
static ReporterIon |
ReporterIon.iTRAQ114
Standard reporter ion iTRAQ 114.
|
static ReporterIon |
ReporterIon.iTRAQ115
Standard reporter ion iTRAQ 115.
|
static ReporterIon |
ReporterIon.iTRAQ116
Standard reporter ion iTRAQ 116.
|
static ReporterIon |
ReporterIon.iTRAQ117
Standard reporter ion iTRAQ 117.
|
static ReporterIon |
ReporterIon.iTRAQ118
Standard reporter ion iTRAQ 118.
|
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).
|
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_etd
Standard reporter ion TMT 126 obtained by etd fragmentation.
|
static ReporterIon |
ReporterIon.TMT126_hcd
Standard reporter ion TMT 126 obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT126_old
Standard reporter ion for an old TMT 126.
|
static ReporterIon |
ReporterIon.TMT127_etd
Standard reporter ion TMT 127 obtained by etd fragmentation.
|
static ReporterIon |
ReporterIon.TMT127_hcd
Standard reporter ion TMT 127 obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT127_old
Standard reporter ion for an old TMT 127.
|
static ReporterIon |
ReporterIon.TMT127C_hcd
Standard reporter ion TMT 127C obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT127N_hcd
Standard reporter ion TMT 127N obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT128_etd
Standard reporter ion TMT 128 obtained by etd fragmentation.
|
static ReporterIon |
ReporterIon.TMT128_hcd
Standard reporter ion TMT 128 obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT128_old
Standard reporter ion for an old TMT 128.
|
static ReporterIon |
ReporterIon.TMT128C_hcd
Standard reporter ion TMT 128C obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT128N_hcd
Standard reporter ion TMT 128N obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT129_etd
Standard reporter ion TMT 129 obtained by etd fragmentation.
|
static ReporterIon |
ReporterIon.TMT129_hcd
Standard reporter ion TMT 129 obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT129_old
Standard reporter ion for an old TMT 129.
|
static ReporterIon |
ReporterIon.TMT129C_hcd
Standard reporter ion TMT 129C obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT129N_hcd
Standard reporter ion TMT 129N obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT130_etd
Standard reporter ion TMT 130 obtained by etd fragmentation.
|
static ReporterIon |
ReporterIon.TMT130_hcd
Standard reporter ion TMT 130 obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT130_old
Standard reporter ion for an old TMT 130.
|
static ReporterIon |
ReporterIon.TMT130C_hcd
Standard reporter ion TMT 130C obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT130N_hcd
Standard reporter ion TMT 130N obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT131_etd
Standard reporter ion TMT 131 obtained by etd fragmentation.
|
static ReporterIon |
ReporterIon.TMT131_hcd
Standard reporter ion TMT 131 obtained by hcd fragmentation.
|
static ReporterIon |
ReporterIon.TMT131_old
Standard reporter ion for an old TMT 131.
|
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
boolean |
ReporterIon.isSameAs(ReporterIon anotherReporterIon)
Compares the current reporter ion with another one based on their masses.
|
Modifier and Type | Method and Description |
---|---|
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.
|
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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