public class ReporterIon extends Ion
Ion.IonType
Modifier and Type | Field and Description |
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static ReporterIon |
ACE_K_126
Standard reporter ion for lysine acetylation (PMID: 18338905).
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static ReporterIon |
ACE_K_143
Standard reporter ion for lysine acetylation (PMID: 18338905).
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static ReporterIon |
iTRAQ_145
Standard reporter ion iTRAQ (reporter + balancer).
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static ReporterIon |
iTRAQ_305
Standard reporter ion iTRAQ (reporter + balancer).
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static ReporterIon |
iTRAQ113
Standard reporter ion iTRAQ 113.
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static ReporterIon |
iTRAQ114
Standard reporter ion iTRAQ 114.
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static ReporterIon |
iTRAQ115
Standard reporter ion iTRAQ 115.
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static ReporterIon |
iTRAQ116
Standard reporter ion iTRAQ 116.
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static ReporterIon |
iTRAQ117
Standard reporter ion iTRAQ 117.
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static ReporterIon |
iTRAQ118
Standard reporter ion iTRAQ 118.
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static ReporterIon |
iTRAQ119
Standard reporter ion iTRAQ 119.
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static ReporterIon |
iTRAQ121
Standard reporter ion iTRAQ 121.
|
static ReporterIon |
PHOSPHO_Y
Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).
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static ReporterIon |
TMT_226
Standard reporter ion TMT (reporter + balancer).
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static ReporterIon |
TMT_230
Standard reporter ion TMT (reporter + balancer).
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static ReporterIon |
TMT126_etd
Standard reporter ion TMT 126 obtained by etd fragmentation.
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static ReporterIon |
TMT126_hcd
Standard reporter ion TMT 126 obtained by hcd fragmentation.
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static ReporterIon |
TMT126_old
Standard reporter ion for an old TMT 126.
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static ReporterIon |
TMT127_etd
Standard reporter ion TMT 127 obtained by etd fragmentation.
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static ReporterIon |
TMT127_hcd
Standard reporter ion TMT 127 obtained by hcd fragmentation.
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static ReporterIon |
TMT127_old
Standard reporter ion for an old TMT 127.
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static ReporterIon |
TMT127C_hcd
Standard reporter ion TMT 127C obtained by hcd fragmentation.
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static ReporterIon |
TMT127N_hcd
Standard reporter ion TMT 127N obtained by hcd fragmentation.
|
static ReporterIon |
TMT128_etd
Standard reporter ion TMT 128 obtained by etd fragmentation.
|
static ReporterIon |
TMT128_hcd
Standard reporter ion TMT 128 obtained by hcd fragmentation.
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static ReporterIon |
TMT128_old
Standard reporter ion for an old TMT 128.
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static ReporterIon |
TMT128C_hcd
Standard reporter ion TMT 128C obtained by hcd fragmentation.
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static ReporterIon |
TMT128N_hcd
Standard reporter ion TMT 128N obtained by hcd fragmentation.
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static ReporterIon |
TMT129_etd
Standard reporter ion TMT 129 obtained by etd fragmentation.
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static ReporterIon |
TMT129_hcd
Standard reporter ion TMT 129 obtained by hcd fragmentation.
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static ReporterIon |
TMT129_old
Standard reporter ion for an old TMT 129.
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static ReporterIon |
TMT129C_hcd
Standard reporter ion TMT 129C obtained by hcd fragmentation.
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static ReporterIon |
TMT129N_hcd
Standard reporter ion TMT 129N obtained by hcd fragmentation.
|
static ReporterIon |
TMT130_etd
Standard reporter ion TMT 130 obtained by etd fragmentation.
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static ReporterIon |
TMT130_hcd
Standard reporter ion TMT 130 obtained by hcd fragmentation.
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static ReporterIon |
TMT130_old
Standard reporter ion for an old TMT 130.
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static ReporterIon |
TMT130C_hcd
Standard reporter ion TMT 130C obtained by hcd fragmentation.
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static ReporterIon |
TMT130N_hcd
Standard reporter ion TMT 130N obtained by hcd fragmentation.
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static ReporterIon |
TMT131_etd
Standard reporter ion TMT 131 obtained by etd fragmentation.
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static ReporterIon |
TMT131_hcd
Standard reporter ion TMT 131 obtained by hcd fragmentation.
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static ReporterIon |
TMT131_old
Standard reporter ion for an old TMT 131.
|
theoreticMass, type
Constructor and Description |
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ReporterIon(String name,
double mass)
Constructor for a user-defined reporter ion.
|
ReporterIon(String name,
double mass,
boolean save)
Constructor for a user-defined reporter ion.
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Modifier and Type | Method and Description |
---|---|
static Set<String> |
getImplementedIons()
Returns an arraylist of possible subtypes.
|
int |
getIndex()
Returns the index of a reporter ion.
|
String |
getName()
This method returns the name of the reporter ion.
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ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the possible neutral losses of this ion type.
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static ArrayList<Integer> |
getPossibleSubtypes()
Returns an arraylist of possible subtypes.
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CvTerm |
getPrideCvTerm()
Returns the pride cv term adapted to the fragment ion.
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static ReporterIon |
getReporterIon(int subType)
Returns the reporter ion indexed by the given index.
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static ReporterIon |
getReporterIon(String name)
Returns the reporter ion corresponding to the given name.
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int |
getSubType()
Returns the ion subtype.
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String |
getSubTypeAsString()
Returns the subtype as string.
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double |
getTheoreticMass()
Returns the theoretic mass.
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boolean |
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.
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boolean |
isSameAs(ReporterIon anotherReporterIon)
Compares the current reporter ion with another one based on their masses.
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void |
setMass(double referenceMass)
Method to set the mass of the reporter ion.
|
void |
setName(String name)
Setter for the ion name.
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getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMz, getType, getTypeAsString, getTypeAsString, setTheoreticMass
addUrParam, getParameterKey, getUrParam
public static final ReporterIon iTRAQ113
public static final ReporterIon iTRAQ114
public static final ReporterIon iTRAQ115
public static final ReporterIon iTRAQ116
public static final ReporterIon iTRAQ117
public static final ReporterIon iTRAQ118
public static final ReporterIon iTRAQ119
public static final ReporterIon iTRAQ121
public static final ReporterIon iTRAQ_145
public static final ReporterIon iTRAQ_305
public static final ReporterIon TMT126_old
public static final ReporterIon TMT127_old
public static final ReporterIon TMT128_old
public static final ReporterIon TMT129_old
public static final ReporterIon TMT130_old
public static final ReporterIon TMT131_old
public static final ReporterIon TMT126_hcd
public static final ReporterIon TMT126_etd
public static final ReporterIon TMT127_hcd
public static final ReporterIon TMT127_etd
public static final ReporterIon TMT127N_hcd
public static final ReporterIon TMT127C_hcd
public static final ReporterIon TMT128_hcd
public static final ReporterIon TMT128_etd
public static final ReporterIon TMT128N_hcd
public static final ReporterIon TMT128C_hcd
public static final ReporterIon TMT129_hcd
public static final ReporterIon TMT129_etd
public static final ReporterIon TMT129N_hcd
public static final ReporterIon TMT129C_hcd
public static final ReporterIon TMT130_hcd
public static final ReporterIon TMT130_etd
public static final ReporterIon TMT130N_hcd
public static final ReporterIon TMT130C_hcd
public static final ReporterIon TMT131_hcd
public static final ReporterIon TMT131_etd
public static final ReporterIon TMT_230
public static final ReporterIon TMT_226
public static final ReporterIon ACE_K_126
public static final ReporterIon ACE_K_143
public static final ReporterIon PHOSPHO_Y
public ReporterIon(String name, double mass)
name
- name of the reporter ion. Should be unique to the ion.mass
- theoretic mass of the reporter ionpublic ReporterIon(String name, double mass, boolean save)
name
- name of the reporter ion. Should be unique to the ion.mass
- theoretic mass of the reporter ionsave
- if true the reporter ion will be saved in the static map for later reusepublic String getName()
public void setName(String name)
name
- the new ion namepublic void setMass(double referenceMass)
referenceMass
- the mass where the reporter ions should be foundpublic CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public boolean isSameAs(ReporterIon anotherReporterIon)
anotherReporterIon
- the other reporter ionpublic int getIndex()
public int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static ReporterIon getReporterIon(int subType)
subType
- the index of interestpublic static ReporterIon getReporterIon(String name)
name
- the name of the reporter ionpublic static Set<String> getImplementedIons()
public static ArrayList<Integer> getPossibleSubtypes()
public ArrayList<NeutralLoss> getNeutralLosses()
Ion
getNeutralLosses
in class Ion
public boolean isSameAs(Ion anotherIon)
Ion
public double getTheoreticMass()
Ion
getTheoreticMass
in class Ion
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