[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map
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static StringList | getIsotopeMatrixAsStringList (const int itraq_type, const IsotopeMatrices &isotope_corrections) |
| convert isotope correction matrix to stringlist More...
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static void | updateIsotopeMatrixFromStringList (const int itraq_type, const StringList &channels, IsotopeMatrices &isotope_corrections) |
| convert strings to isotope correction matrix rows More...
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static void | initChannelMap (const int itraq_type, ChannelMapType &map) |
| information about an iTRAQ channel More...
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static void | updateChannelMap (const StringList &active_channels, ChannelMapType &map) |
| activate & annotate channels More...
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static Matrix< double > | translateIsotopeMatrix (const int &itraq_type, const IsotopeMatrices &isotope_corrections) |
| translate isotope correction matrix in -2,-1,+1,+2 form into 114,115,116,117 format More...
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static const Int | CHANNEL_COUNT [] |
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static const Int | CHANNELS_FOURPLEX [4][1] |
| channel names for 4plex( 114, 115, 116, 117) More...
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static const Int | CHANNELS_EIGHTPLEX [8][1] |
| channel names for 8plex( 113, 114, 115, 116, 117, 118, 119, 121) More...
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static const Int | CHANNELS_TMT_SIXPLEX [6][1] |
| channel names for 6plex TMT with CID fragmentation( 126, 127, 128, 129, 130, 131) More...
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static const double | ISOTOPECORRECTIONS_FOURPLEX [4][4] |
| default isotope correction matrix (4 plex) More...
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static const double | ISOTOPECORRECTIONS_EIGHTPLEX [8][4] |
| default isotope correction matrix (8 plex) More...
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static const double | ISOTOPECORRECTIONS_TMT_SIXPLEX [6][4] |
| default isotope correction matrix (6 plex TMT) More...
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Protected Attributes inherited from DefaultParamHandler |
Param | param_ |
| Container for current parameters. More...
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Param | defaults_ |
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
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std::vector< String > | subsections_ |
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
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String | error_name_ |
| Name that is displayed in error messages during the parameter checking. More...
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bool | check_defaults_ |
| If this member is set to false no checking if parameters in done;. More...
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bool | warn_empty_defaults_ |
| If this member is set to false no warning is emitted when defaults are empty;. More...
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[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map
[experimental class] This class supports 4 and 8 channel iTRAQ and 6 channel TMT and will optionally do peak picking before the quantitation step. Quantitation is done by adding all signals within a small delta around the expected m/z of each channel. When all channels are found to be empty, the ConsensusFeature is not created. No post-processing is done here. Use ItraqQuantifier for that!
Parameters of this class are:
Name | Type | Default | Restrictions | Description |
select_activation |
string | High-energy collision-induced dissociation |
Collision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, | Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering. |
reporter_mass_shift |
float | 0.1 |
min: 1e-08 max: 0.5 | Allowed shift (left to right) in Da from the expected position. |
channel_active |
string list | [114:liver, 117:lung] |
| Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format :, e.g. "114:myref","115:liver". |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.