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PILISModel Class Reference

This class implements the simulation of the spectra from PILIS. More...

#include <OpenMS/ANALYSIS/ID/PILISModel.h>

Inheritance diagram for PILISModel:
DefaultParamHandler

Public Member Functions

PILISModeloperator= (const PILISModel &mode)
 assignment operator More...
 
Constructors and destructors
 PILISModel ()
 default constructor More...
 
 PILISModel (const PILISModel &model)
 copy constructor More...
 
virtual ~PILISModel ()
 destructor More...
 
Accessors
void train (const RichPeakSpectrum &, const AASequence &peptide, UInt charge)
 performs a training step; needs as parameters a spectrum with annotated sequence and charge More...
 
void readFromFile (const String &filename)
 
void writeGraphMLFile (const String &filename)
 writes the HMM to the given file in the GraphML format. A detailed description of the GraphML format can be found under http://graphml.graphdrawing.org/ More...
 
void writeToFile (const String &filename)
 
void init (bool generate_models=true)
 
void getSpectrum (RichPeakSpectrum &spec, const AASequence &peptide, UInt charge)
 simulates a spectrum with the model of the given peptide and charge and writes it to the given PeakSpectrum More...
 
void evaluate ()
 this method evaluates the model after training; it should be called after all training steps with train More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Protected Member Functions

bool getInitialTransitionProbabilities_ (std::vector< DoubleReal > &bb_init, std::vector< DoubleReal > &cr_init, std::vector< DoubleReal > &sc_init, DoubleReal &precursor_init, const std::vector< DoubleReal > &bb_charges, const std::vector< DoubleReal > &sc_charges, const AASequence &peptide)
 get the initial transition probabilities from the proton dist, returns true if charge remote is enabled More...
 
DoubleReal getAvailableBackboneCharge_ (const AASequence &ion, Residue::ResidueType res_type, int charge)
 
void addPeaks_ (DoubleReal mz, int charge, DoubleReal mz_offset, DoubleReal intensity, RichPeakSpectrum &spectrum, const IsotopeDistribution &id, const String &name)
 add peaks to spectrum More...
 
void parseHMMModel_ (const TextFile::ConstIterator &begin, const TextFile::ConstIterator &end, HiddenMarkovModel &hmm, Param &param)
 parse the base model More...
 
void writeParameters_ (std::ostream &os, const Param &param)
 write parameters of the model More...
 
void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

HiddenMarkovModel hmm_
 base model used More...
 
ProtonDistributionModel prot_dist_
 proton distribution model More...
 
TheoreticalSpectrumGenerator tsg_
 theoretical spectrum generator (needed for training/aligning and spectrum intensity extraction) More...
 
bool valid_
 true if the instance is valid More...
 
Map< DoubleReal, std::vector
< RichPeak1D > > 
peaks_
 stores the peaks of a spectrum More...
 
SpectrumAlignment spectra_aligner_
 the alignment algorithm used More...
 
PILISNeutralLossModel precursor_model_cr_
 precursor model used More...
 
PILISNeutralLossModel precursor_model_cd_
 
PILISNeutralLossModel a_ion_losses_cr_
 
PILISNeutralLossModel a_ion_losses_cd_
 
PILISNeutralLossModel b_ion_losses_cr_
 
PILISNeutralLossModel b_ion_losses_cd_
 
PILISNeutralLossModel b2_ion_losses_cr_
 
PILISNeutralLossModel b2_ion_losses_cd_
 
PILISNeutralLossModel y_ion_losses_cr_
 
PILISNeutralLossModel y_ion_losses_cd_
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

This class implements the simulation of the spectra from PILIS.

PILIS uses a HMM based structure to model the population of fragment ions from a peptide. The spectrum generator can be accessed via the getSpectrum method.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
upper_mz float2000  Max m/z value of product ions in the simulated spectrum
lower_mz float200  Lowest m/z value of product ions in the simulated spectrum
charge_remote_threshold float0.3  If the probability for the proton at the N-terminus is lower than this value, enable charge-remote pathways
charge_directed_threshold float0.3  Limit the proton availability at the N-terminus to at least this value for charge-directed pathways
model_depth int10  The number of explicitly modeled backbone cleavages from N-terminus and C-terminus, would be 9 for the default value
visible_model_depth int50  The maximal possible size of a peptide to be modeled
precursor_mass_tolerance float3  Mass tolerance of the precursor peak, used to identify the precursor peak and its loss peaks for training
fragment_mass_tolerance float0.3  Peak mass tolerance of the product ions, used to identify the ions for training
variable_modifications string list[Oxidation (M), Carbamyl (K)] 15dB-biotin (C), 2-succinyl (C), 2HPG (R), 3-deoxyglucosone (R), 3sulfo (N-term), 4-ONE (C), 4-ONE (H), 4-ONE (K), 4-ONE+Delta:H(-2)O(-1) (C), 4-ONE+Delta:H(-2)O(-1) (H), 4-ONE+Delta:H(-2)O(-1) (K), 4AcAllylGal (C), ADP-Ribosyl (C), ADP-Ribosyl (E), ADP-Ribosyl (N), ADP-Ribosyl (R), ADP-Ribosyl (S), AEBS (H), AEBS (K), AEBS (S), AEBS (Y), AEC-MAEC (S), AEC-MAEC (T), AEC-MAEC:2H(4) (S), AEC-MAEC:2H(4) (T), AROD (C), AccQTag (K), AccQTag (N-term), Acetyl (C), Acetyl (H), Acetyl (K), Acetyl (N-term), Acetyl (S), Acetyl (T), Acetyl (Y), Acetyl:2H(3) (K), Acetyl:2H(3) (N-term), Ala->Asp (A), Ala->Glu (A), Ala->Gly (A), Ala->Pro (A), Ala->Ser (A), Ala->Thr (A), Ala->Val (A), Amidated (C-term), Amidine (K), Amidine (N-term), Amidino (C), Amino (Y), Ammonia-loss (N), Ammonia-loss (N-term C), Ammonium (C-term), Ammonium (D), Ammonium (E), Archaeol (C), Arg->Cys (R), Arg->Gln (R), Arg->GluSA (R), Arg->Gly (R), Arg->His (R), Arg->Ile (R), Arg->Lys (R), Arg->Met (R), Arg->Npo (R), Arg->Orn (R), Arg->Pro (R), Arg->Ser (R), Arg->Thr (R), Arg->Trp (R), Arg2PG (R), Argbiotinhydrazide (R), Asn->Asp (N), Asn->His (N), Asn->Ile (N), Asn->Lys (N), Asn->Ser (N), Asn->Thr (N), Asn->Tyr (N), Asp->Ala (D), Asp->Asn (D), Asp->Glu (D), Asp->Gly (D), Asp->His (D), Asp->Tyr (D), Asp->Val (D), Atto495Maleimide (C), BADGE (C), BDMAPP (H), BDMAPP (K), BDMAPP (W), BDMAPP (Y), BHAc (K), BHT (C), BHT (H), BHT (K), BHTOH (C), BHTOH (H), BHTOH (K), BITC (C), BITC (K), BITC (N-term), BMOE (C), Bacillosamine (N), Benzoyl (K), Benzoyl (N-term), Biotin (K), Biotin (N-term), Biotin-HPDP (C), Biotin-PEG-PRA (M), Biotin-PEO-Amine (D), Biotin-PEO-Amine (E), Biotin-PEO4-hydrazide (C-term), Biotin-maleimide (C), Biotin-phenacyl (C), Biotin-phenacyl (H), Biotin-phenacyl (S), BisANS (K), Bodipy (C), Bromo (F), Bromo (H), Bromo (W), Bromobimane (C), C8-QAT (K), C8-QAT (N-term), CAF (N-term), CAMthiopropanoyl (K), CHDH (D), CLIP_TRAQ_1 (K), CLIP_TRAQ_1 (N-term), CLIP_TRAQ_1 (Y), CLIP_TRAQ_2 (K), CLIP_TRAQ_2 (N-term), CLIP_TRAQ_2 (Y), CLIP_TRAQ_3 (K), CLIP_TRAQ_3 (N-term), CLIP_TRAQ_3 (Y), CLIP_TRAQ_4 (K), CLIP_TRAQ_4 (N-term), CLIP_TRAQ_4 (Y), Can-FP-biotin (S), Can-FP-biotin (T), Can-FP-biotin (Y), Carbamidomethyl (C), Carbamidomethyl (D), Carbamidomethyl (E), Carbamidomethyl (H), Carbamidomethyl (K), Carbamidomethyl (N-term), CarbamidomethylDTT (C), Carbamyl (C), Carbamyl (K), Carbamyl (M), Carbamyl (N-term), Carbamyl (R), Carbamyl (S), Carbamyl (T), Carbamyl (Y), Carbofuran (S), Carboxy (D), Carboxy (E), Carboxy (K), Carboxy (W), Carboxyethyl (K), Carboxymethyl (C), Carboxymethyl (K), Carboxymethyl (N-term), Carboxymethyl (W), Carboxymethyl:13C(2) (C), CarboxymethylDTT (C), Cation:Ag (C-term), Cation:Ag (D), Cation:Ag (E), Cation:Ca[II] (C-term), Cation:Ca[II] (D), Cation:Ca[II] (E), Cation:Cu[I] (C-term), Cation:Cu[I] (D), Cation:Cu[I] (E), Cation:Fe[II] (C-term), Cation:Fe[II] (D), Cation:Fe[II] (E), Cation:K (C-term), Cation:K (D), Cation:K (E), Cation:Li (C-term), Cation:Li (D), Cation:Li (E), Cation:Mg[II] (C-term), Cation:Mg[II] (D), Cation:Mg[II] (E), Cation:Na (C-term), Cation:Na (D), Cation:Na (E), Cation:Ni[II] (C-term), Cation:Ni[II] (D), Cation:Ni[II] (E), Cation:Zn[II] (C-term), Cation:Zn[II] (D), Cation:Zn[II] (E), Chlorination (Y), Chlorpyrifos (S), Chlorpyrifos (T), Chlorpyrifos (Y), ChromoBiotin (K), CoenzymeA (C), Crotonaldehyde (C), Crotonaldehyde (H), Crotonaldehyde (K), CuSMo (C), Cy3b-maleimide (C), CyDye-Cy3 (C), CyDye-Cy5 (C), Cyano (C), Cys->Arg (C), Cys->Dha (C), Cys->Gly (C), Cys->Oxoalanine (C), Cys->Phe (C), Cys->Ser (C), Cys->Trp (C), Cys->Tyr (C), Cys->ethylaminoAla (C), Cys->methylaminoAla (C), Cysteinyl (C), Cytopiloyne (C), Cytopiloyne (K), Cytopiloyne (N-term), Cytopiloyne (P), Cytopiloyne (R), Cytopiloyne (S), Cytopiloyne (Y), Cytopiloyne+water (C), Cytopiloyne+water (K), Cytopiloyne+water (N-term), Cytopiloyne+water (R), Cytopiloyne+water (S), Cytopiloyne+water (T), Cytopiloyne+water (Y), DAET (S), DAET (T), DFDNB (K), DFDNB (N), DFDNB (Q), DFDNB (R), DHP (C), DNPS (C), DNPS (W), DTBP (K), DTBP (N), DTBP (Q), DTBP (R), DTT_C (C), DTT_C:2H(6) (C), DTT_ST (S), DTT_ST (T), DTT_ST:2H(6) (S), DTT_ST:2H(6) (T), Dansyl (K), Dansyl (N-term), DeStreak (C), Deamidated (N), Deamidated (Q), Deamidated (R), Deamidated:18O(1) (N), Deamidated:18O(1) (Q), Decanoyl (S), Decanoyl (T), Dehydrated (D), Dehydrated (N-term C), Dehydrated (S), Dehydrated (T), Dehydrated (Y), Dehydro (C), Delta:H(1)O(-1)18O(1) (N), Delta:H(2)C(2) (H), Delta:H(2)C(2) (K), Delta:H(2)C(3) (K), Delta:H(2)C(3)O(1) (K), Delta:H(2)C(3)O(1) (R), Delta:H(2)C(5) (K), Delta:H(4)C(2) (H), Delta:H(4)C(2) (K), Delta:H(4)C(2)O(-1)S(1) (S), Delta:H(4)C(3) (H), Delta:H(4)C(3) (K), Delta:H(4)C(3)O(1) (C), Delta:H(4)C(3)O(1) (H), Delta:H(4)C(3)O(1) (K), Delta:H(4)C(6) (K), Delta:H(5)C(2) (P), Delta:H(6)C(6)O(1) (K), Delta:H(8)C(6)O(2) (K), Delta:Hg(1) (C), Delta:S(-1)Se(1) (C), Delta:S(-1)Se(1) (M), Delta:Se(1) (C), Deoxy (D), Deoxy (S), Deoxy (T), Dethiomethyl (M), Diacylglycerol (C), Dibromo (Y), Didehydro (C-term K), Didehydro (S), Didehydro (T), Didehydro (Y), Didehydroretinylidene (K), Diethyl (K), Diethyl (N-term), Dihydroxyimidazolidine (R), Diiodo (Y), Diironsubcluster (C), Diisopropylphosphate (K), Diisopropylphosphate (S), Diisopropylphosphate (T), Diisopropylphosphate (Y), Dimethyl (K), Dimethyl (N), Dimethyl (N-term), Dimethyl (R), Dimethyl:2H(4) (K), Dimethyl:2H(4) (N-term), Dimethyl:2H(4)13C(2) (K), Dimethyl:2H(4)13C(2) (N-term), Dimethyl:2H(6)13C(2) (K), Dimethyl:2H(6)13C(2) (N-term), Dimethyl:2H(6)13C(2) (R), DimethylArsino (C), DimethylamineGMBS (C), DimethylpyrroleAdduct (K), Dioxidation (C), Dioxidation (F), Dioxidation (K), Dioxidation (M), Dioxidation (P), Dioxidation (R), Dioxidation (W), Dioxidation (Y), Diphthamide (H), Dipyrrolylmethanemethyl (C), DyLight-maleimide (C), EDT-iodoacetyl-PEO-biotin (S), EDT-iodoacetyl-PEO-biotin (T), EDT-maleimide-PEO-biotin (S), EDT-maleimide-PEO-biotin (T), EQAT (C), EQAT:2H(5) (C), EQIGG (K), ESP (K), ESP (N-term), ESP:2H(10) (K), ESP:2H(10) (N-term), Ethanedithiol (S), Ethanedithiol (T), Ethanolamine (C-term), Ethanolamine (D), Ethanolamine (E), Ethanolyl (C), Ethanolyl (K), Ethanolyl (R), Ethoxyformyl (H), Ethyl (C-term), Ethyl (D), Ethyl (E), Ethyl (K), Ethyl (N-term), EthylAmide (N), EthylAmide (Q), ExacTagAmine (K), ExacTagThiol (C), FAD (C), FAD (H), FAD (Y), FMN (S), FMN (T), FMNC (C), FMNH (C), FMNH (H), FNEM (C), FP-Biotin (K), FP-Biotin (S), FP-Biotin (T), FP-Biotin (Y), FTC (C), FTC (K), FTC (P), FTC (R), FTC (S), Farnesyl (C), Fluorescein (C), Fluoro (F), Fluoro (W), Fluoro (Y), Formyl (K), Formyl (N-term), Formyl (S), Formyl (T), G-H1 (R), GIST-Quat (K), GIST-Quat (N-term), GIST-Quat:2H(3) (K), GIST-Quat:2H(3) (N-term), GIST-Quat:2H(6) (K), GIST-Quat:2H(6) (N-term), GIST-Quat:2H(9) (K), GIST-Quat:2H(9) (N-term), GalNAzBiotin (N), GalNAzBiotin (S), GalNAzBiotin (T), Galactosyl (K), GeranylGeranyl (C), Gln->Arg (Q), Gln->Glu (Q), Gln->His (Q), Gln->Leu (Q), Gln->Lys (Q), Gln->Pro (Q), Gln->pyro-Glu (N-term Q), Glu (E), Glu->Ala (E), Glu->Asp (E), Glu->Gln (E), Glu->Gly (E), Glu->Lys (E), Glu->Val (E), Glu->pyro-Glu (N-term E), GluGlu (E), GluGluGlu (E), GluGluGluGlu (E), Glucosylgalactosyl (K), Glucuronyl (S), Glutathione (C), Gly->Ala (G), Gly->Arg (G), Gly->Asp (G), Gly->Cys (G), Gly->Glu (G), Gly->Ser (G), Gly->Trp (G), Gly->Val (G), Gly-loss+Amide (C-term G), GlyGly (C), GlyGly (K), GlyGly (S), GlyGly (T), Glycerophospho (S), GlycerylPE (E), Glycosyl (P), Guanidinyl (K), HMVK (C), HNE (C), HNE (H), HNE (K), HNE+Delta:H(2) (C), HNE+Delta:H(2) (H), HNE+Delta:H(2) (K), HNE-BAHAH (C), HNE-BAHAH (H), HNE-BAHAH (K), HNE-Delta:H(2)O (C), HNE-Delta:H(2)O (H), HNE-Delta:H(2)O (K), HPG (R), Heme (C), Heme (H), Hep (K), Hep (N), Hep (Q), Hep (R), Hep (S), Hep (T), Hex (C), Hex (K), Hex (N), Hex (N-term), Hex (R), Hex (T), Hex (W), Hex (Y), Hex(1)HexNAc(1)NeuAc(1) (N), Hex(1)HexNAc(1)NeuAc(1) (S), Hex(1)HexNAc(1)NeuAc(1) (T), Hex(1)HexNAc(1)NeuAc(2) (N), Hex(1)HexNAc(1)NeuAc(2) (S), Hex(1)HexNAc(1)NeuAc(2) (T), Hex(1)HexNAc(1)dHex(1) (N), Hex(1)HexNAc(2) (N), Hex(1)HexNAc(2)Pent(1) (N), Hex(1)HexNAc(2)dHex(1) (N), Hex(1)HexNAc(2)dHex(1)Pent(1) (N), Hex(1)HexNAc(2)dHex(2) (N), Hex(2) (K), Hex(2) (R), Hex(2)HexNAc(2) (N), Hex(2)HexNAc(2)Pent(1) (N), Hex(2)HexNAc(2)dHex(1) (N), Hex(3) (N), Hex(3)HexNAc(1)Pent(1) (N), Hex(3)HexNAc(2) (N), Hex(3)HexNAc(2)P(1) (N), Hex(3)HexNAc(4) (N), Hex(4)HexNAc(4) (N), Hex(5)HexNAc(2) (N), Hex(5)HexNAc(4) (N), Hex1HexNAc1 (S), Hex1HexNAc1 (T), HexN (K), HexN (N), HexN (T), HexN (W), HexNAc (N), HexNAc (S), HexNAc (T), HexNAc(1)dHex(1) (N), HexNAc(1)dHex(2) (N), HexNAc(2) (N), HexNAc(2)dHex(1) (N), HexNAc(2)dHex(2) (N), His->Arg (H), His->Asn (H), His->Asp (H), His->Gln (H), His->Leu (H), His->Pro (H), His->Tyr (H), Hydroxycinnamyl (C), Hydroxyfarnesyl (C), Hydroxyheme (E), Hydroxymethyl (N), HydroxymethylOP (K), Hydroxytrimethyl (K), Hypusine (K), IBTP (C), ICAT-C (C), ICAT-C:13C(9) (C), ICAT-D (C), ICAT-D:2H(8) (C), ICAT-G (C), ICAT-G:2H(8) (C), ICAT-H (C), ICAT-H:13C(6) (C), ICPL (K), ICPL (N-term), ICPL:13C(6) (K), ICPL:13C(6) (N-term), ICPL:13C(6)2H(4) (K), ICPL:13C(6)2H(4) (N-term), ICPL:2H(4) (K), ICPL:2H(4) (N-term), IDEnT (C), IED-Biotin (C), IGBP (C), IGBP:13C(2) (C), IMID (K), IMID:2H(4) (K), ISD_z+2_ion (N-term), Ile->Arg (I), Ile->Asn (I), Ile->Lys (I), Ile->Met (I), Ile->Phe (I), Ile->Ser (I), Ile->Thr (I), Ile->Val (I), Iminobiotin (K), Iminobiotin (N-term), Iodo (H), Iodo (Y), IodoU-AMP (F), IodoU-AMP (W), IodoU-AMP (Y), Isopropylphospho (S), Isopropylphospho (T), Isopropylphospho (Y), LG-Hlactam-K (K), LG-Hlactam-R (R), LG-anhydrolactam (K), LG-anhydrolactam (N-term), LG-anhyropyrrole (K), LG-anhyropyrrole (N-term), LG-lactam-K (K), LG-lactam-R (R), LG-pyrrole (K), LG-pyrrole (N-term), Label:13C(1)2H(3) (M), Label:13C(1)2H(3)+Oxidation (M), Label:13C(4)15N(2)+GlyGly (K), Label:13C(5) (P), Label:13C(5)15N(1) (M), Label:13C(5)15N(1) (P), Label:13C(5)15N(1) (V), Label:13C(6) (I), Label:13C(6) (K), Label:13C(6) (L), Label:13C(6) (R), Label:13C(6)+Acetyl (K), Label:13C(6)+Dimethyl (K), Label:13C(6)+GlyGly (K), Label:13C(6)15N(1) (I), Label:13C(6)15N(1) (L), Label:13C(6)15N(2) (K), Label:13C(6)15N(2)+Acetyl (K), Label:13C(6)15N(2)+Dimethyl (K), Label:13C(6)15N(2)+GlyGly (K), Label:13C(6)15N(4) (R), Label:13C(8)15N(2) (R), Label:13C(9) (F), Label:13C(9) (Y), Label:13C(9)+Phospho (Y), Label:13C(9)15N(1) (F), Label:15N(1) (A), Label:15N(1) (C), Label:15N(1) (D), Label:15N(1) (E), Label:15N(1) (F), Label:15N(1) (G), Label:15N(1) (I), Label:15N(1) (L), Label:15N(1) (M), Label:15N(1) (P), Label:15N(1) (S), Label:15N(1) (T), Label:15N(1) (V), Label:15N(1) (Y), Label:15N(2) (K), Label:15N(2) (N), Label:15N(2) (Q), Label:15N(2) (W), Label:15N(2)2H(9) (K), Label:15N(3) (H), Label:15N(4) (R), Label:18O(1) (C-term), Label:18O(1) (S), Label:18O(1) (T), Label:18O(1) (Y), Label:18O(2) (C-term), Label:2H(3) (L), Label:2H(4) (F), Label:2H(4) (K), Label:2H(4) (Y), Label:2H(4)+Acetyl (K), Label:2H(4)+GlyGly (K), Label:2H(9)13C(6)15N(2) (K), Leu->Arg (L), Leu->Gln (L), Leu->His (L), Leu->Met (L), Leu->MetOx (L), Leu->Phe (L), Leu->Pro (L), Leu->Ser (L), Leu->Trp (L), Leu->Val (L), LeuArgGlyGly (K), Lipoyl (K), Lys->Allysine (K), Lys->AminoadipicAcid (K), Lys->Arg (K), Lys->Asn (K), Lys->CamCys (K), Lys->Gln (K), Lys->Glu (K), Lys->Ile (K), Lys->Met (K), Lys->MetOx (K), Lys->Thr (K), Lysbiotinhydrazide (K), MDCC (C), MG-H1 (R), MTSL (C), Maleimide-PEO2-Biotin (C), Malonyl (C), Malonyl (S), Menadione (C), Menadione (K), Menadione-HQ (C), Menadione-HQ (K), MercaptoEthanol (S), MercaptoEthanol (T), Met->Aha (M), Met->Arg (M), Met->Hpg (M), Met->Hse (C-term M), Met->Hsl (C-term M), Met->Ile (M), Met->Leu (M), Met->Lys (M), Met->Thr (M), Met->Val (M), Methyl (C), Methyl (C-term), Methyl (D), Methyl (E), Methyl (H), Methyl (I), Methyl (K), Methyl (L), Methyl (N), Methyl (N-term), Methyl (Q), Methyl (R), Methyl (S), Methyl (T), Methyl+Acetyl:2H(3) (K), Methyl+Deamidated (N), Methyl+Deamidated (Q), Methyl-PEO12-Maleimide (C), Methyl:2H(2) (K), Methyl:2H(3) (C-term), Methyl:2H(3) (D), Methyl:2H(3) (E), Methyl:2H(3)13C(1) (R), Methylamine (S), Methylamine (T), Methylmalonylation (S), Methylphosphonate (S), Methylphosphonate (T), Methylphosphonate (Y), Methylpyrroline (K), Methylthio (C), Methylthio (D), Methylthio (N), Molybdopterin (C), MolybdopterinGD (C), MolybdopterinGD (D), MolybdopterinGD+Delta:S(-1)Se(1) (C), Myristoyl (C), Myristoyl (K), Myristoyl (N-term G), NA-LNO2 (C), NA-LNO2 (H), NA-OA-NO2 (C), NA-OA-NO2 (H), NBS (W), NBS:13C(6) (W), NDA (K), NDA (N-term), NEIAA (C), NEIAA (Y), NEIAA:2H(5) (C), NEIAA:2H(5) (Y), NEM:2H(5) (C), NHS-LC-Biotin (K), NHS-LC-Biotin (N-term), NIC (N-term), NIPCAM (C), NO_SMX_SEMD (C), NO_SMX_SIMD (C), NO_SMX_SMCT (C), Nethylmaleimide (C), Nethylmaleimide+water (C), Nethylmaleimide+water (K), Nitro (W), Nitro (Y), Nitrosyl (C), Nmethylmaleimide (C), Nmethylmaleimide (K), Nmethylmaleimide+water (C), O-Diethylphosphate (C), O-Diethylphosphate (H), O-Diethylphosphate (K), O-Diethylphosphate (S), O-Diethylphosphate (T), O-Diethylphosphate (Y), O-Dimethylphosphate (S), O-Dimethylphosphate (T), O-Dimethylphosphate (Y), O-Ethylphosphate (S), O-Ethylphosphate (T), O-Ethylphosphate (Y), O-Isopropylmethylphosphonate (S), O-Isopropylmethylphosphonate (T), O-Isopropylmethylphosphonate (Y), O-Methylphosphate (S), O-Methylphosphate (T), O-Methylphosphate (Y), O-pinacolylmethylphosphonate (H), O-pinacolylmethylphosphonate (K), O-pinacolylmethylphosphonate (S), O-pinacolylmethylphosphonate (T), O-pinacolylmethylphosphonate (Y), Octanoyl (S), Octanoyl (T), OxArgBiotin (R), OxArgBiotinRed (R), OxLysBiotin (K), OxLysBiotinRed (K), OxProBiotin (P), OxProBiotinRed (P), Oxidation (C), Oxidation (C-term G), Oxidation (D), Oxidation (F), Oxidation (H), Oxidation (K), Oxidation (M), Oxidation (N), Oxidation (P), Oxidation (R), Oxidation (W), Oxidation (Y), PEITC (C), PEITC (K), PEITC (N-term), PEO-Iodoacetyl-LC-Biotin (C), PET (S), PET (T), PGA1-biotin (C), Palmitoleyl (C), Palmitoleyl (S), Palmitoleyl (T), Palmitoyl (C), Palmitoyl (K), Palmitoyl (S), Palmitoyl (T), Pentylamine (Q), PentylamineBiotin (Q), Phe->CamCys (F), Phe->Cys (F), Phe->Ile (F), Phe->Ser (F), Phe->Tyr (F), Phe->Val (F), Phenylisocyanate (N-term), Phenylisocyanate:2H(5) (N-term), Phospho (C), Phospho (D), Phospho (H), Phospho (R), Phospho (S), Phospho (T), Phospho (Y), PhosphoHex (S), PhosphoHexNAc (S), PhosphoUridine (H), PhosphoUridine (Y), Phosphoadenosine (H), Phosphoadenosine (K), Phosphoadenosine (T), Phosphoadenosine (Y), Phosphoguanosine (H), Phosphoguanosine (K), Phosphopantetheine (S), Phosphopropargyl (S), Phosphopropargyl (T), Phosphopropargyl (Y), PhosphoribosyldephosphoCoA (S), Phycocyanobilin (C), Phycoerythrobilin (C), Phytochromobilin (C), Piperidine (K), Piperidine (N-term), Pro->Ala (P), Pro->Arg (P), Pro->Gln (P), Pro->His (P), Pro->Leu (P), Pro->Pyrrolidinone (P), Pro->Pyrrolidone (P), Pro->Ser (P), Pro->Thr (P), Pro->pyro-Glu (P), Propargylamine (C-term), Propargylamine (D), Propargylamine (E), Propionamide (C), Propionamide:2H(3) (C), Propionyl (K), Propionyl (N-term), Propionyl (S), Propionyl:13C(3) (K), Propionyl:13C(3) (N-term), PropylNAGthiazoline (C), Puromycin (C-term), PyMIC (N-term), PyridoxalPhosphate (K), Pyridylacetyl (K), Pyridylacetyl (N-term), Pyridylethyl (C), Pyro-carbamidomethyl (N-term C), PyruvicAcidIminyl (K), QAT (C), QAT:2H(3) (C), QEQTGG (K), QQQTGG (K), Quinone (W), Quinone (Y), RNPXlink1 (C), RNPXlink2 (F), RNPXlink2 (K), RNPXlink2 (L), RNPXlink3 (C), RNPXlink3 (F), RNPXlink4 (C), RNPXlink5 (F), RNPXlink5 (Y), Retinylidene (K), SMA (K), SMA (N-term), SMCC-maleimide (C), SPITC (K), SPITC (N-term), SPITC:13C(6) (K), SPITC:13C(6) (N-term), SUMO2135 (K), SUMO3549 (K), Ser->Ala (S), Ser->Arg (S), Ser->Asn (S), Ser->Cys (S), Ser->Gly (S), Ser->Ile (S), Ser->Phe (S), Ser->Pro (S), Ser->Thr (S), Ser->Trp (S), Ser->Tyr (S), Succinyl (K), Succinyl (N-term), Succinyl:13C(4) (K), Succinyl:13C(4) (N-term), Succinyl:2H(4) (K), Succinyl:2H(4) (N-term), SulfanilicAcid (C-term), SulfanilicAcid (D), SulfanilicAcid (E), SulfanilicAcid:13C(6) (C-term), SulfanilicAcid:13C(6) (D), SulfanilicAcid:13C(6) (E), Sulfide (C), Sulfide (D), Sulfo (C), Sulfo (S), Sulfo (T), Sulfo (Y), Sulfo-NHS-LC-LC-Biotin (K), Sulfo-NHS-LC-LC-Biotin (N-term), SulfoGMBS (C), TMAB (K), TMAB (N-term), TMAB:2H(9) (K), TMAB:2H(9) (N-term), TMPP-Ac (N-term), TMT (K), TMT (N-term), TMT2plex (K), TMT2plex (N-term), TMT6plex (K), TMT6plex (N-term), TNBS (K), TNBS (N-term), Thioacyl (K), Thioacyl (N-term), Thiophos-S-S-biotin (S), Thiophos-S-S-biotin (T), Thiophos-S-S-biotin (Y), Thiophospho (S), Thiophospho (T), Thiophospho (Y), Thr->Ala (T), Thr->Arg (T), Thr->Asn (T), Thr->Ile (T), Thr->Lys (T), Thr->Met (T), Thr->Pro (T), Thr->Ser (T), Thrbiotinhydrazide (T), Thyroxine (Y), Triiodo (Y), Triiodothyronine (Y), Trimethyl (K), Trimethyl (R), Trioxidation (C), Trp->Arg (W), Trp->Cys (W), Trp->Gly (W), Trp->Hydroxykynurenin (W), Trp->Kynurenin (W), Trp->Leu (W), Trp->Oxolactone (W), Trp->Ser (W), Tyr->Asn (Y), Tyr->Asp (Y), Tyr->Cys (Y), Tyr->Dha (Y), Tyr->His (Y), Tyr->Phe (Y), Tyr->Ser (Y), VFQQQTGG (K), VIEVYQEQTGG (K), Val->Ala (V), Val->Asp (V), Val->Glu (V), Val->Gly (V), Val->Ile (V), Val->Met (V), Val->Phe (V), Xlink:B10621 (C), Xlink:DMP (K), Xlink:DMP-s (K), Xlink:SSD (K), ZGB (K), ZGB (N-term), a-type-ion (C-term), cGMP (C), cGMP (S), cGMP+RMP-loss (C), cGMP+RMP-loss (S), cysTMT (C), cysTMT6plex (C), dHex (S), dHex (T), dHex(1)Hex(3)HexNAc(4) (N), dHex(1)Hex(4)HexNAc(4) (N), dHex(1)Hex(5)HexNAc(4) (N), dNIC (N-term), dichlorination (Y), ethylamino (S), ethylamino (T), glucosone (R), iTRAQ4plex (K), iTRAQ4plex (N-term), iTRAQ4plex (Y), iTRAQ4plex114 (K), iTRAQ4plex114 (N-term), iTRAQ4plex114 (Y), iTRAQ4plex115 (K), iTRAQ4plex115 (N-term), iTRAQ4plex115 (Y), iTRAQ8plex (K), iTRAQ8plex (N-term), iTRAQ8plex (Y), iTRAQ8plex:13C(6)15N(2) (K), iTRAQ8plex:13C(6)15N(2) (N-term), iTRAQ8plex:13C(6)15N(2) (Y), lapachenole (C), mTRAQ (K), mTRAQ (N-term), mTRAQ (Y), mTRAQ:13C(3)15N(1) (K), mTRAQ:13C(3)15N(1) (N-term), mTRAQ:13C(3)15N(1) (Y), maleimide (C), maleimide (K), maleimide3 (C), maleimide3 (K), maleimide5 (C), maleimide5 (K), probiotinhydrazide (P), pyrophospho (S), pyrophospho (T), sulfo+amino (Y), thioacylPA (K), trifluoro (L)Modifications which should be included in the model, represented by PSI-MOD accessions.
fixed_modifications string list[] 15dB-biotin (C), 2-succinyl (C), 2HPG (R), 3-deoxyglucosone (R), 3sulfo (N-term), 4-ONE (C), 4-ONE (H), 4-ONE (K), 4-ONE+Delta:H(-2)O(-1) (C), 4-ONE+Delta:H(-2)O(-1) (H), 4-ONE+Delta:H(-2)O(-1) (K), 4AcAllylGal (C), ADP-Ribosyl (C), ADP-Ribosyl (E), ADP-Ribosyl (N), ADP-Ribosyl (R), ADP-Ribosyl (S), AEBS (H), AEBS (K), AEBS (S), AEBS (Y), AEC-MAEC (S), AEC-MAEC (T), AEC-MAEC:2H(4) (S), AEC-MAEC:2H(4) (T), AROD (C), AccQTag (K), AccQTag (N-term), Acetyl (C), Acetyl (H), Acetyl (K), Acetyl (N-term), Acetyl (S), Acetyl (T), Acetyl (Y), Acetyl:2H(3) (K), Acetyl:2H(3) (N-term), Ala->Asp (A), Ala->Glu (A), Ala->Gly (A), Ala->Pro (A), Ala->Ser (A), Ala->Thr (A), Ala->Val (A), Amidated (C-term), Amidine (K), Amidine (N-term), Amidino (C), Amino (Y), Ammonia-loss (N), Ammonia-loss (N-term C), Ammonium (C-term), Ammonium (D), Ammonium (E), Archaeol (C), Arg->Cys (R), Arg->Gln (R), Arg->GluSA (R), Arg->Gly (R), Arg->His (R), Arg->Ile (R), Arg->Lys (R), Arg->Met (R), Arg->Npo (R), Arg->Orn (R), Arg->Pro (R), Arg->Ser (R), Arg->Thr (R), Arg->Trp (R), Arg2PG (R), Argbiotinhydrazide (R), Asn->Asp (N), Asn->His (N), Asn->Ile (N), Asn->Lys (N), Asn->Ser (N), Asn->Thr (N), Asn->Tyr (N), Asp->Ala (D), Asp->Asn (D), Asp->Glu (D), Asp->Gly (D), Asp->His (D), Asp->Tyr (D), Asp->Val (D), Atto495Maleimide (C), BADGE (C), BDMAPP (H), BDMAPP (K), BDMAPP (W), BDMAPP (Y), BHAc (K), BHT (C), BHT (H), BHT (K), BHTOH (C), BHTOH (H), BHTOH (K), BITC (C), BITC (K), BITC (N-term), BMOE (C), Bacillosamine (N), Benzoyl (K), Benzoyl (N-term), Biotin (K), Biotin (N-term), Biotin-HPDP (C), Biotin-PEG-PRA (M), Biotin-PEO-Amine (D), Biotin-PEO-Amine (E), Biotin-PEO4-hydrazide (C-term), Biotin-maleimide (C), Biotin-phenacyl (C), Biotin-phenacyl (H), Biotin-phenacyl (S), BisANS (K), Bodipy (C), Bromo (F), Bromo (H), Bromo (W), Bromobimane (C), C8-QAT (K), C8-QAT (N-term), CAF (N-term), CAMthiopropanoyl (K), CHDH (D), CLIP_TRAQ_1 (K), CLIP_TRAQ_1 (N-term), CLIP_TRAQ_1 (Y), CLIP_TRAQ_2 (K), CLIP_TRAQ_2 (N-term), CLIP_TRAQ_2 (Y), CLIP_TRAQ_3 (K), CLIP_TRAQ_3 (N-term), CLIP_TRAQ_3 (Y), CLIP_TRAQ_4 (K), CLIP_TRAQ_4 (N-term), CLIP_TRAQ_4 (Y), Can-FP-biotin (S), Can-FP-biotin (T), Can-FP-biotin (Y), Carbamidomethyl (C), Carbamidomethyl (D), Carbamidomethyl (E), Carbamidomethyl (H), Carbamidomethyl (K), Carbamidomethyl (N-term), CarbamidomethylDTT (C), Carbamyl (C), Carbamyl (K), Carbamyl (M), Carbamyl (N-term), Carbamyl (R), Carbamyl (S), Carbamyl (T), Carbamyl (Y), Carbofuran (S), Carboxy (D), Carboxy (E), Carboxy (K), Carboxy (W), Carboxyethyl (K), Carboxymethyl (C), Carboxymethyl (K), Carboxymethyl (N-term), Carboxymethyl (W), Carboxymethyl:13C(2) (C), CarboxymethylDTT (C), Cation:Ag (C-term), Cation:Ag (D), Cation:Ag (E), Cation:Ca[II] (C-term), Cation:Ca[II] (D), Cation:Ca[II] (E), Cation:Cu[I] (C-term), Cation:Cu[I] (D), Cation:Cu[I] (E), Cation:Fe[II] (C-term), Cation:Fe[II] (D), Cation:Fe[II] (E), Cation:K (C-term), Cation:K (D), Cation:K (E), Cation:Li (C-term), Cation:Li (D), Cation:Li (E), Cation:Mg[II] (C-term), Cation:Mg[II] (D), Cation:Mg[II] (E), Cation:Na (C-term), Cation:Na (D), Cation:Na (E), Cation:Ni[II] (C-term), Cation:Ni[II] (D), Cation:Ni[II] (E), Cation:Zn[II] (C-term), Cation:Zn[II] (D), Cation:Zn[II] (E), Chlorination (Y), Chlorpyrifos (S), Chlorpyrifos (T), Chlorpyrifos (Y), ChromoBiotin (K), CoenzymeA (C), Crotonaldehyde (C), Crotonaldehyde (H), Crotonaldehyde (K), CuSMo (C), Cy3b-maleimide (C), CyDye-Cy3 (C), CyDye-Cy5 (C), Cyano (C), Cys->Arg (C), Cys->Dha (C), Cys->Gly (C), Cys->Oxoalanine (C), Cys->Phe (C), Cys->Ser (C), Cys->Trp (C), Cys->Tyr (C), Cys->ethylaminoAla (C), Cys->methylaminoAla (C), Cysteinyl (C), Cytopiloyne (C), Cytopiloyne (K), Cytopiloyne (N-term), Cytopiloyne (P), Cytopiloyne (R), Cytopiloyne (S), Cytopiloyne (Y), Cytopiloyne+water (C), Cytopiloyne+water (K), Cytopiloyne+water (N-term), Cytopiloyne+water (R), Cytopiloyne+water (S), Cytopiloyne+water (T), Cytopiloyne+water (Y), DAET (S), DAET (T), DFDNB (K), DFDNB (N), DFDNB (Q), DFDNB (R), DHP (C), DNPS (C), DNPS (W), DTBP (K), DTBP (N), DTBP (Q), DTBP (R), DTT_C (C), DTT_C:2H(6) (C), DTT_ST (S), DTT_ST (T), DTT_ST:2H(6) (S), DTT_ST:2H(6) (T), Dansyl (K), Dansyl (N-term), DeStreak (C), Deamidated (N), Deamidated (Q), Deamidated (R), Deamidated:18O(1) (N), Deamidated:18O(1) (Q), Decanoyl (S), Decanoyl (T), Dehydrated (D), Dehydrated (N-term C), Dehydrated (S), Dehydrated (T), Dehydrated (Y), Dehydro (C), Delta:H(1)O(-1)18O(1) (N), Delta:H(2)C(2) (H), Delta:H(2)C(2) (K), Delta:H(2)C(3) (K), Delta:H(2)C(3)O(1) (K), Delta:H(2)C(3)O(1) (R), Delta:H(2)C(5) (K), Delta:H(4)C(2) (H), Delta:H(4)C(2) (K), Delta:H(4)C(2)O(-1)S(1) (S), Delta:H(4)C(3) (H), Delta:H(4)C(3) (K), Delta:H(4)C(3)O(1) (C), Delta:H(4)C(3)O(1) (H), Delta:H(4)C(3)O(1) (K), Delta:H(4)C(6) (K), Delta:H(5)C(2) (P), Delta:H(6)C(6)O(1) (K), Delta:H(8)C(6)O(2) (K), Delta:Hg(1) (C), Delta:S(-1)Se(1) (C), Delta:S(-1)Se(1) (M), Delta:Se(1) (C), Deoxy (D), Deoxy (S), Deoxy (T), Dethiomethyl (M), Diacylglycerol (C), Dibromo (Y), Didehydro (C-term K), Didehydro (S), Didehydro (T), Didehydro (Y), Didehydroretinylidene (K), Diethyl (K), Diethyl (N-term), Dihydroxyimidazolidine (R), Diiodo (Y), Diironsubcluster (C), Diisopropylphosphate (K), Diisopropylphosphate (S), Diisopropylphosphate (T), Diisopropylphosphate (Y), Dimethyl (K), Dimethyl (N), Dimethyl (N-term), Dimethyl (R), Dimethyl:2H(4) (K), Dimethyl:2H(4) (N-term), Dimethyl:2H(4)13C(2) (K), Dimethyl:2H(4)13C(2) (N-term), Dimethyl:2H(6)13C(2) (K), Dimethyl:2H(6)13C(2) (N-term), Dimethyl:2H(6)13C(2) (R), DimethylArsino (C), DimethylamineGMBS (C), DimethylpyrroleAdduct (K), Dioxidation (C), Dioxidation (F), Dioxidation (K), Dioxidation (M), Dioxidation (P), Dioxidation (R), Dioxidation (W), Dioxidation (Y), Diphthamide (H), Dipyrrolylmethanemethyl (C), DyLight-maleimide (C), EDT-iodoacetyl-PEO-biotin (S), EDT-iodoacetyl-PEO-biotin (T), EDT-maleimide-PEO-biotin (S), EDT-maleimide-PEO-biotin (T), EQAT (C), EQAT:2H(5) (C), EQIGG (K), ESP (K), ESP (N-term), ESP:2H(10) (K), ESP:2H(10) (N-term), Ethanedithiol (S), Ethanedithiol (T), Ethanolamine (C-term), Ethanolamine (D), Ethanolamine (E), Ethanolyl (C), Ethanolyl (K), Ethanolyl (R), Ethoxyformyl (H), Ethyl (C-term), Ethyl (D), Ethyl (E), Ethyl (K), Ethyl (N-term), EthylAmide (N), EthylAmide (Q), ExacTagAmine (K), ExacTagThiol (C), FAD (C), FAD (H), FAD (Y), FMN (S), FMN (T), FMNC (C), FMNH (C), FMNH (H), FNEM (C), FP-Biotin (K), FP-Biotin (S), FP-Biotin (T), FP-Biotin (Y), FTC (C), FTC (K), FTC (P), FTC (R), FTC (S), Farnesyl (C), Fluorescein (C), Fluoro (F), Fluoro (W), Fluoro (Y), Formyl (K), Formyl (N-term), Formyl (S), Formyl (T), G-H1 (R), GIST-Quat (K), GIST-Quat (N-term), GIST-Quat:2H(3) (K), GIST-Quat:2H(3) (N-term), GIST-Quat:2H(6) (K), GIST-Quat:2H(6) (N-term), GIST-Quat:2H(9) (K), GIST-Quat:2H(9) (N-term), GalNAzBiotin (N), GalNAzBiotin (S), GalNAzBiotin (T), Galactosyl (K), GeranylGeranyl (C), Gln->Arg (Q), Gln->Glu (Q), Gln->His (Q), Gln->Leu (Q), Gln->Lys (Q), Gln->Pro (Q), Gln->pyro-Glu (N-term Q), Glu (E), Glu->Ala (E), Glu->Asp (E), Glu->Gln (E), Glu->Gly (E), Glu->Lys (E), Glu->Val (E), Glu->pyro-Glu (N-term E), GluGlu (E), GluGluGlu (E), GluGluGluGlu (E), Glucosylgalactosyl (K), Glucuronyl (S), Glutathione (C), Gly->Ala (G), Gly->Arg (G), Gly->Asp (G), Gly->Cys (G), Gly->Glu (G), Gly->Ser (G), Gly->Trp (G), Gly->Val (G), Gly-loss+Amide (C-term G), GlyGly (C), GlyGly (K), GlyGly (S), GlyGly (T), Glycerophospho (S), GlycerylPE (E), Glycosyl (P), Guanidinyl (K), HMVK (C), HNE (C), HNE (H), HNE (K), HNE+Delta:H(2) (C), HNE+Delta:H(2) (H), HNE+Delta:H(2) (K), HNE-BAHAH (C), HNE-BAHAH (H), HNE-BAHAH (K), HNE-Delta:H(2)O (C), HNE-Delta:H(2)O (H), HNE-Delta:H(2)O (K), HPG (R), Heme (C), Heme (H), Hep (K), Hep (N), Hep (Q), Hep (R), Hep (S), Hep (T), Hex (C), Hex (K), Hex (N), Hex (N-term), Hex (R), Hex (T), Hex (W), Hex (Y), Hex(1)HexNAc(1)NeuAc(1) (N), Hex(1)HexNAc(1)NeuAc(1) (S), Hex(1)HexNAc(1)NeuAc(1) (T), Hex(1)HexNAc(1)NeuAc(2) (N), Hex(1)HexNAc(1)NeuAc(2) (S), Hex(1)HexNAc(1)NeuAc(2) (T), Hex(1)HexNAc(1)dHex(1) (N), Hex(1)HexNAc(2) (N), Hex(1)HexNAc(2)Pent(1) (N), Hex(1)HexNAc(2)dHex(1) (N), Hex(1)HexNAc(2)dHex(1)Pent(1) (N), Hex(1)HexNAc(2)dHex(2) (N), Hex(2) (K), Hex(2) (R), Hex(2)HexNAc(2) (N), Hex(2)HexNAc(2)Pent(1) (N), Hex(2)HexNAc(2)dHex(1) (N), Hex(3) (N), Hex(3)HexNAc(1)Pent(1) (N), Hex(3)HexNAc(2) (N), Hex(3)HexNAc(2)P(1) (N), Hex(3)HexNAc(4) (N), Hex(4)HexNAc(4) (N), Hex(5)HexNAc(2) (N), Hex(5)HexNAc(4) (N), Hex1HexNAc1 (S), Hex1HexNAc1 (T), HexN (K), HexN (N), HexN (T), HexN (W), HexNAc (N), HexNAc (S), HexNAc (T), HexNAc(1)dHex(1) (N), HexNAc(1)dHex(2) (N), HexNAc(2) (N), HexNAc(2)dHex(1) (N), HexNAc(2)dHex(2) (N), His->Arg (H), His->Asn (H), His->Asp (H), His->Gln (H), His->Leu (H), His->Pro (H), His->Tyr (H), Hydroxycinnamyl (C), Hydroxyfarnesyl (C), Hydroxyheme (E), Hydroxymethyl (N), HydroxymethylOP (K), Hydroxytrimethyl (K), Hypusine (K), IBTP (C), ICAT-C (C), ICAT-C:13C(9) (C), ICAT-D (C), ICAT-D:2H(8) (C), ICAT-G (C), ICAT-G:2H(8) (C), ICAT-H (C), ICAT-H:13C(6) (C), ICPL (K), ICPL (N-term), ICPL:13C(6) (K), ICPL:13C(6) (N-term), ICPL:13C(6)2H(4) (K), ICPL:13C(6)2H(4) (N-term), ICPL:2H(4) (K), ICPL:2H(4) (N-term), IDEnT (C), IED-Biotin (C), IGBP (C), IGBP:13C(2) (C), IMID (K), IMID:2H(4) (K), ISD_z+2_ion (N-term), Ile->Arg (I), Ile->Asn (I), Ile->Lys (I), Ile->Met (I), Ile->Phe (I), Ile->Ser (I), Ile->Thr (I), Ile->Val (I), Iminobiotin (K), Iminobiotin (N-term), Iodo (H), Iodo (Y), IodoU-AMP (F), IodoU-AMP (W), IodoU-AMP (Y), Isopropylphospho (S), Isopropylphospho (T), Isopropylphospho (Y), LG-Hlactam-K (K), LG-Hlactam-R (R), LG-anhydrolactam (K), LG-anhydrolactam (N-term), LG-anhyropyrrole (K), LG-anhyropyrrole (N-term), LG-lactam-K (K), LG-lactam-R (R), LG-pyrrole (K), LG-pyrrole (N-term), Label:13C(1)2H(3) (M), Label:13C(1)2H(3)+Oxidation (M), Label:13C(4)15N(2)+GlyGly (K), Label:13C(5) (P), Label:13C(5)15N(1) (M), Label:13C(5)15N(1) (P), Label:13C(5)15N(1) (V), Label:13C(6) (I), Label:13C(6) (K), Label:13C(6) (L), Label:13C(6) (R), Label:13C(6)+Acetyl (K), Label:13C(6)+Dimethyl (K), Label:13C(6)+GlyGly (K), Label:13C(6)15N(1) (I), Label:13C(6)15N(1) (L), Label:13C(6)15N(2) (K), Label:13C(6)15N(2)+Acetyl (K), Label:13C(6)15N(2)+Dimethyl (K), Label:13C(6)15N(2)+GlyGly (K), Label:13C(6)15N(4) (R), Label:13C(8)15N(2) (R), Label:13C(9) (F), Label:13C(9) (Y), Label:13C(9)+Phospho (Y), Label:13C(9)15N(1) (F), Label:15N(1) (A), Label:15N(1) (C), Label:15N(1) (D), Label:15N(1) (E), Label:15N(1) (F), Label:15N(1) (G), Label:15N(1) (I), Label:15N(1) (L), Label:15N(1) (M), Label:15N(1) (P), Label:15N(1) (S), Label:15N(1) (T), Label:15N(1) (V), Label:15N(1) (Y), Label:15N(2) (K), Label:15N(2) (N), Label:15N(2) (Q), Label:15N(2) (W), Label:15N(2)2H(9) (K), Label:15N(3) (H), Label:15N(4) (R), Label:18O(1) (C-term), Label:18O(1) (S), Label:18O(1) (T), Label:18O(1) (Y), Label:18O(2) (C-term), Label:2H(3) (L), Label:2H(4) (F), Label:2H(4) (K), Label:2H(4) (Y), Label:2H(4)+Acetyl (K), Label:2H(4)+GlyGly (K), Label:2H(9)13C(6)15N(2) (K), Leu->Arg (L), Leu->Gln (L), Leu->His (L), Leu->Met (L), Leu->MetOx (L), Leu->Phe (L), Leu->Pro (L), Leu->Ser (L), Leu->Trp (L), Leu->Val (L), LeuArgGlyGly (K), Lipoyl (K), Lys->Allysine (K), Lys->AminoadipicAcid (K), Lys->Arg (K), Lys->Asn (K), Lys->CamCys (K), Lys->Gln (K), Lys->Glu (K), Lys->Ile (K), Lys->Met (K), Lys->MetOx (K), Lys->Thr (K), Lysbiotinhydrazide (K), MDCC (C), MG-H1 (R), MTSL (C), Maleimide-PEO2-Biotin (C), Malonyl (C), Malonyl (S), Menadione (C), Menadione (K), Menadione-HQ (C), Menadione-HQ (K), MercaptoEthanol (S), MercaptoEthanol (T), Met->Aha (M), Met->Arg (M), Met->Hpg (M), Met->Hse (C-term M), Met->Hsl (C-term M), Met->Ile (M), Met->Leu (M), Met->Lys (M), Met->Thr (M), Met->Val (M), Methyl (C), Methyl (C-term), Methyl (D), Methyl (E), Methyl (H), Methyl (I), Methyl (K), Methyl (L), Methyl (N), Methyl (N-term), Methyl (Q), Methyl (R), Methyl (S), Methyl (T), Methyl+Acetyl:2H(3) (K), Methyl+Deamidated (N), Methyl+Deamidated (Q), Methyl-PEO12-Maleimide (C), Methyl:2H(2) (K), Methyl:2H(3) (C-term), Methyl:2H(3) (D), Methyl:2H(3) (E), Methyl:2H(3)13C(1) (R), Methylamine (S), Methylamine (T), Methylmalonylation (S), Methylphosphonate (S), Methylphosphonate (T), Methylphosphonate (Y), Methylpyrroline (K), Methylthio (C), Methylthio (D), Methylthio (N), Molybdopterin (C), MolybdopterinGD (C), MolybdopterinGD (D), MolybdopterinGD+Delta:S(-1)Se(1) (C), Myristoyl (C), Myristoyl (K), Myristoyl (N-term G), NA-LNO2 (C), NA-LNO2 (H), NA-OA-NO2 (C), NA-OA-NO2 (H), NBS (W), NBS:13C(6) (W), NDA (K), NDA (N-term), NEIAA (C), NEIAA (Y), NEIAA:2H(5) (C), NEIAA:2H(5) (Y), NEM:2H(5) (C), NHS-LC-Biotin (K), NHS-LC-Biotin (N-term), NIC (N-term), NIPCAM (C), NO_SMX_SEMD (C), NO_SMX_SIMD (C), NO_SMX_SMCT (C), Nethylmaleimide (C), Nethylmaleimide+water (C), Nethylmaleimide+water (K), Nitro (W), Nitro (Y), Nitrosyl (C), Nmethylmaleimide (C), Nmethylmaleimide (K), Nmethylmaleimide+water (C), O-Diethylphosphate (C), O-Diethylphosphate (H), O-Diethylphosphate (K), O-Diethylphosphate (S), O-Diethylphosphate (T), O-Diethylphosphate (Y), O-Dimethylphosphate (S), O-Dimethylphosphate (T), O-Dimethylphosphate (Y), O-Ethylphosphate (S), O-Ethylphosphate (T), O-Ethylphosphate (Y), O-Isopropylmethylphosphonate (S), O-Isopropylmethylphosphonate (T), O-Isopropylmethylphosphonate (Y), O-Methylphosphate (S), O-Methylphosphate (T), O-Methylphosphate (Y), O-pinacolylmethylphosphonate (H), O-pinacolylmethylphosphonate (K), O-pinacolylmethylphosphonate (S), O-pinacolylmethylphosphonate (T), O-pinacolylmethylphosphonate (Y), Octanoyl (S), Octanoyl (T), OxArgBiotin (R), OxArgBiotinRed (R), OxLysBiotin (K), OxLysBiotinRed (K), OxProBiotin (P), OxProBiotinRed (P), Oxidation (C), Oxidation (C-term G), Oxidation (D), Oxidation (F), Oxidation (H), Oxidation (K), Oxidation (M), Oxidation (N), Oxidation (P), Oxidation (R), Oxidation (W), Oxidation (Y), PEITC (C), PEITC (K), PEITC (N-term), PEO-Iodoacetyl-LC-Biotin (C), PET (S), PET (T), PGA1-biotin (C), Palmitoleyl (C), Palmitoleyl (S), Palmitoleyl (T), Palmitoyl (C), Palmitoyl (K), Palmitoyl (S), Palmitoyl (T), Pentylamine (Q), PentylamineBiotin (Q), Phe->CamCys (F), Phe->Cys (F), Phe->Ile (F), Phe->Ser (F), Phe->Tyr (F), Phe->Val (F), Phenylisocyanate (N-term), Phenylisocyanate:2H(5) (N-term), Phospho (C), Phospho (D), Phospho (H), Phospho (R), Phospho (S), Phospho (T), Phospho (Y), PhosphoHex (S), PhosphoHexNAc (S), PhosphoUridine (H), PhosphoUridine (Y), Phosphoadenosine (H), Phosphoadenosine (K), Phosphoadenosine (T), Phosphoadenosine (Y), Phosphoguanosine (H), Phosphoguanosine (K), Phosphopantetheine (S), Phosphopropargyl (S), Phosphopropargyl (T), Phosphopropargyl (Y), PhosphoribosyldephosphoCoA (S), Phycocyanobilin (C), Phycoerythrobilin (C), Phytochromobilin (C), Piperidine (K), Piperidine (N-term), Pro->Ala (P), Pro->Arg (P), Pro->Gln (P), Pro->His (P), Pro->Leu (P), Pro->Pyrrolidinone (P), Pro->Pyrrolidone (P), Pro->Ser (P), Pro->Thr (P), Pro->pyro-Glu (P), Propargylamine (C-term), Propargylamine (D), Propargylamine (E), Propionamide (C), Propionamide:2H(3) (C), Propionyl (K), Propionyl (N-term), Propionyl (S), Propionyl:13C(3) (K), Propionyl:13C(3) (N-term), PropylNAGthiazoline (C), Puromycin (C-term), PyMIC (N-term), PyridoxalPhosphate (K), Pyridylacetyl (K), Pyridylacetyl (N-term), Pyridylethyl (C), Pyro-carbamidomethyl (N-term C), PyruvicAcidIminyl (K), QAT (C), QAT:2H(3) (C), QEQTGG (K), QQQTGG (K), Quinone (W), Quinone (Y), RNPXlink1 (C), RNPXlink2 (F), RNPXlink2 (K), RNPXlink2 (L), RNPXlink3 (C), RNPXlink3 (F), RNPXlink4 (C), RNPXlink5 (F), RNPXlink5 (Y), Retinylidene (K), SMA (K), SMA (N-term), SMCC-maleimide (C), SPITC (K), SPITC (N-term), SPITC:13C(6) (K), SPITC:13C(6) (N-term), SUMO2135 (K), SUMO3549 (K), Ser->Ala (S), Ser->Arg (S), Ser->Asn (S), Ser->Cys (S), Ser->Gly (S), Ser->Ile (S), Ser->Phe (S), Ser->Pro (S), Ser->Thr (S), Ser->Trp (S), Ser->Tyr (S), Succinyl (K), Succinyl (N-term), Succinyl:13C(4) (K), Succinyl:13C(4) (N-term), Succinyl:2H(4) (K), Succinyl:2H(4) (N-term), SulfanilicAcid (C-term), SulfanilicAcid (D), SulfanilicAcid (E), SulfanilicAcid:13C(6) (C-term), SulfanilicAcid:13C(6) (D), SulfanilicAcid:13C(6) (E), Sulfide (C), Sulfide (D), Sulfo (C), Sulfo (S), Sulfo (T), Sulfo (Y), Sulfo-NHS-LC-LC-Biotin (K), Sulfo-NHS-LC-LC-Biotin (N-term), SulfoGMBS (C), TMAB (K), TMAB (N-term), TMAB:2H(9) (K), TMAB:2H(9) (N-term), TMPP-Ac (N-term), TMT (K), TMT (N-term), TMT2plex (K), TMT2plex (N-term), TMT6plex (K), TMT6plex (N-term), TNBS (K), TNBS (N-term), Thioacyl (K), Thioacyl (N-term), Thiophos-S-S-biotin (S), Thiophos-S-S-biotin (T), Thiophos-S-S-biotin (Y), Thiophospho (S), Thiophospho (T), Thiophospho (Y), Thr->Ala (T), Thr->Arg (T), Thr->Asn (T), Thr->Ile (T), Thr->Lys (T), Thr->Met (T), Thr->Pro (T), Thr->Ser (T), Thrbiotinhydrazide (T), Thyroxine (Y), Triiodo (Y), Triiodothyronine (Y), Trimethyl (K), Trimethyl (R), Trioxidation (C), Trp->Arg (W), Trp->Cys (W), Trp->Gly (W), Trp->Hydroxykynurenin (W), Trp->Kynurenin (W), Trp->Leu (W), Trp->Oxolactone (W), Trp->Ser (W), Tyr->Asn (Y), Tyr->Asp (Y), Tyr->Cys (Y), Tyr->Dha (Y), Tyr->His (Y), Tyr->Phe (Y), Tyr->Ser (Y), VFQQQTGG (K), VIEVYQEQTGG (K), Val->Ala (V), Val->Asp (V), Val->Glu (V), Val->Gly (V), Val->Ile (V), Val->Met (V), Val->Phe (V), Xlink:B10621 (C), Xlink:DMP (K), Xlink:DMP-s (K), Xlink:SSD (K), ZGB (K), ZGB (N-term), a-type-ion (C-term), cGMP (C), cGMP (S), cGMP+RMP-loss (C), cGMP+RMP-loss (S), cysTMT (C), cysTMT6plex (C), dHex (S), dHex (T), dHex(1)Hex(3)HexNAc(4) (N), dHex(1)Hex(4)HexNAc(4) (N), dHex(1)Hex(5)HexNAc(4) (N), dNIC (N-term), dichlorination (Y), ethylamino (S), ethylamino (T), glucosone (R), iTRAQ4plex (K), iTRAQ4plex (N-term), iTRAQ4plex (Y), iTRAQ4plex114 (K), iTRAQ4plex114 (N-term), iTRAQ4plex114 (Y), iTRAQ4plex115 (K), iTRAQ4plex115 (N-term), iTRAQ4plex115 (Y), iTRAQ8plex (K), iTRAQ8plex (N-term), iTRAQ8plex (Y), iTRAQ8plex:13C(6)15N(2) (K), iTRAQ8plex:13C(6)15N(2) (N-term), iTRAQ8plex:13C(6)15N(2) (Y), lapachenole (C), mTRAQ (K), mTRAQ (N-term), mTRAQ (Y), mTRAQ:13C(3)15N(1) (K), mTRAQ:13C(3)15N(1) (N-term), mTRAQ:13C(3)15N(1) (Y), maleimide (C), maleimide (K), maleimide3 (C), maleimide3 (K), maleimide5 (C), maleimide5 (K), probiotinhydrazide (P), pyrophospho (S), pyrophospho (T), sulfo+amino (Y), thioacylPA (K), trifluoro (L)Modifications which should replace the unmodified amino acid, represented by PSI-MOD accessions.
min_enhancement_factor float2  Minimal factor for bxyz backbone cleavages.
min_y_ion_intensity float0  Minimal intensity for y ions.
min_b_ion_intensity float0  Minimal intensity for b ions.
min_a_ion_intensity float0  Minimal intensity for a ions.
min_y_loss_intensity float0  Minimal intensity for y ions with neutral loss.
min_b_loss_intensity float0  Minimal intensity for b ions with neutral loss.
side_chain_activation float0.2  Additional activation of proton sitting at side chain, especially important at lysine and histidine residues
pseudo_counts float1e-15  Value which is added for every transition trained of the underlying hidden Markov model
max_isotope int2  Maximal isotope peak which is reported by the model, 0 means all isotope peaks are reported
max_fragment_charge_training int2  Maximal allowed charge states for ions to be considered for training
max_fragment_charge int4  Maximal charge state allowed for fragment ions

Note:

Constructor & Destructor Documentation

default constructor

PILISModel ( const PILISModel model)

copy constructor

virtual ~PILISModel ( )
virtual

destructor

Member Function Documentation

void addPeaks_ ( DoubleReal  mz,
int  charge,
DoubleReal  mz_offset,
DoubleReal  intensity,
RichPeakSpectrum spectrum,
const IsotopeDistribution id,
const String name 
)
protected

add peaks to spectrum

void evaluate ( )

this method evaluates the model after training; it should be called after all training steps with train

DoubleReal getAvailableBackboneCharge_ ( const AASequence ion,
Residue::ResidueType  res_type,
int  charge 
)
protected
bool getInitialTransitionProbabilities_ ( std::vector< DoubleReal > &  bb_init,
std::vector< DoubleReal > &  cr_init,
std::vector< DoubleReal > &  sc_init,
DoubleReal precursor_init,
const std::vector< DoubleReal > &  bb_charges,
const std::vector< DoubleReal > &  sc_charges,
const AASequence peptide 
)
protected

get the initial transition probabilities from the proton dist, returns true if charge remote is enabled

void getSpectrum ( RichPeakSpectrum spec,
const AASequence peptide,
UInt  charge 
)

simulates a spectrum with the model of the given peptide and charge and writes it to the given PeakSpectrum

void init ( bool  generate_models = true)
PILISModel& operator= ( const PILISModel mode)

assignment operator

void parseHMMModel_ ( const TextFile::ConstIterator begin,
const TextFile::ConstIterator end,
HiddenMarkovModel hmm,
Param param 
)
protected

parse the base model

void readFromFile ( const String filename)

reads the model parameters from the given files

Parameters
filenamefilename of the model
void train ( const RichPeakSpectrum ,
const AASequence peptide,
UInt  charge 
)

performs a training step; needs as parameters a spectrum with annotated sequence and charge

void updateMembers_ ( )
protectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

void writeGraphMLFile ( const String filename)

writes the HMM to the given file in the GraphML format. A detailed description of the GraphML format can be found under http://graphml.graphdrawing.org/

void writeParameters_ ( std::ostream &  os,
const Param param 
)
protected

write parameters of the model

void writeToFile ( const String filename)

writes the model parameters into the given files

Parameters
filenamefilename of the base model

Member Data Documentation

PILISNeutralLossModel a_ion_losses_cd_
protected
PILISNeutralLossModel a_ion_losses_cr_
protected
PILISNeutralLossModel b2_ion_losses_cd_
protected
PILISNeutralLossModel b2_ion_losses_cr_
protected
PILISNeutralLossModel b_ion_losses_cd_
protected
PILISNeutralLossModel b_ion_losses_cr_
protected
HiddenMarkovModel hmm_
protected

base model used

Map<DoubleReal, std::vector<RichPeak1D> > peaks_
protected

stores the peaks of a spectrum

PILISNeutralLossModel precursor_model_cd_
protected
PILISNeutralLossModel precursor_model_cr_
protected

precursor model used

ProtonDistributionModel prot_dist_
protected

proton distribution model

SpectrumAlignment spectra_aligner_
protected

the alignment algorithm used

theoretical spectrum generator (needed for training/aligning and spectrum intensity extraction)

bool valid_
protected

true if the instance is valid

PILISNeutralLossModel y_ion_losses_cd_
protected
PILISNeutralLossModel y_ion_losses_cr_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5