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PILISModel Class Reference
[Identification]

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

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

Inheritance diagram for PILISModel:
DefaultParamHandler

List of all members.

Public Member Functions

PILISModel & operator= (const PILISModel &mode)
 assignment operator
Constructors and destructors

 PILISModel ()
 default constructor
 PILISModel (const PILISModel &model)
 copy constructor
virtual ~PILISModel ()
 destructor
Accessors

void train (const RichPeakSpectrum &, const AASequence &peptide, UInt charge)
 performs a training step; needs as parameters a spectrum with annotated sequence and charge
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/
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
void evaluate ()
 this method evaluates the model after training; it should be called after all training steps with train

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
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
void parseHMMModel_ (const TextFile::ConstIterator &begin, const TextFile::ConstIterator &end, HiddenMarkovModel &hmm, Param &param)
 parse the base model
void writeParameters_ (std::ostream &os, const Param &param)
 write parameters of the model
void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method.

Protected Attributes

HiddenMarkovModel hmm_
 base model used
ProtonDistributionModel prot_dist_
 proton distribution model
TheoreticalSpectrumGenerator tsg_
 theoretical spectrum generator (needed for training/aligning and spectrum intensity extraction)
bool valid_
 true if the instance is valid
Map< DoubleReal, std::vector
< RichPeak1D > > 		peaks_
 stores the peaks of a spectrum
SpectrumAlignment spectra_aligner_
 the alignment algorithm used
PILISNeutralLossModel precursor_model_cr_
 precursor model used
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_

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

PILISModel (  ) 

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:
filename filename 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_ (  )  [protected, virtual]

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:
filename filename 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

TheoreticalSpectrumGenerator tsg_ [protected]

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 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1