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MascotGenericFile Class Reference
[File IO]

Mascot input file adapter. More...

#include <OpenMS/FORMAT/MascotGenericFile.h>

Inheritance diagram for MascotGenericFile:
ProgressLogger DefaultParamHandler

List of all members.

Public Member Functions

 MascotGenericFile ()
 constructor
virtual ~MascotGenericFile ()
 constructor
void store (const String &filename, const PeakMap &experiment)
 stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell execution
void store (std::ostream &os, const String &filename, const PeakMap &experiment)
 store the experiment data in a MascotGenericFile; the output is written to the given stream, the filename will be noted in the file
template<typename MapType >
void load (const String &filename, MapType &exp)
std::pair< String, String > getHTTPPeakListEnclosure (const String &filename) const
 enclosing Strings of the peak list body for HTTP submission

Protected Member Functions

void writeParameterHeader_ (const String &name, std::ostream &os)
 writes a parameter header
void writeHeader_ (std::ostream &os)
 writes the full header
void writeSpectrum_ (std::ostream &os, const PeakSpectrum &spec, const String &filename)
 writes the spectrum
void writeMSExperiment_ (std::ostream &os, const String &filename, const PeakMap &experiment)
 writes the MSExperiment
bool getNextSpectrum_ (std::istream &is, std::vector< std::pair< double, double > > &spectrum, UInt &charge, double &precursor_mz, double &precursor_int, double &rt, String &title, Size &line_number)
 reads a spectrum block, the section between 'BEGIN IONS' and 'END IONS' of a mgf file

Detailed Description

Mascot input file adapter.

Creates a file that can be used for Mascot search from a peak list or a whole experiment.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
database stringMSDB  Name of the sequence database
search_type stringMIS MIS, SQ, PMFName of the search type for the query
enzyme stringTrypsin  The enzyme descriptor to the enzyme used for digestion. (Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server).
instrument stringDefault  Instrument definition which specifies the fragmentation rules
missed_cleavages int1 min: 0Number of missed cleavages allowed for the enzyme
precursor_mass_tolerance float3 min: 0Tolerance of the precursor peaks
precursor_error_units stringDa %, ppm, mmu, DaUnits of the precursor mass tolerance
fragment_mass_tolerance float0.3 min: 0Tolerance of the peaks in the fragment spectrum
fragment_error_units stringDa mmu, DaUnits of the fragment peaks tolerance
charges string1,2,3  Allowed charge states, given as a comma separated list of integers
taxonomy stringAll entries  Taxonomy specification of the sequences
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)List of fixed modifications, according to UniMod definitions.
variable_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)Variable modifications given as UniMod definitions.
mass_type stringmonoisotopic monoisotopic, averageDefines the mass type, either monoisotopic or average
number_of_hits int0 min: 0Number of hits which should be returned, if 0 AUTO mode is enabled.
skip_spectrum_charges stringfalse true, falseSometimes precursor charges are given for each spectrum but are wrong, setting this to 'true' does not write any charge information to the spectrum, the general charge information is however kept.
search_title stringOpenMS_search  Sets the title of the search.
username stringOpenMS  Sets the username which is mentioned in the results file.
internal:format stringMascot generic Mascot generic, mzData (.XML), mzML (.mzML)Sets the format type of the peak list, this should not be changed unless you write the header only.
internal:boundary stringGZWgAaYKjHFeUaLOLEIOMq  MIME boundary for parameter header (if using HTTP format)
internal:HTTP_format stringfalse true, falseWrite header with MIME boundaries instead of simple key-value pairs. For HTTP submission only.
internal:content stringall all, peaklist_only, header_onlyUse parameter header + the peak lists with BEGIN IONS... or only one of them.

Note:

Constructor & Destructor Documentation

MascotGenericFile (  ) 

constructor

virtual ~MascotGenericFile (  )  [virtual]

constructor

Member Function Documentation

std::pair<String, String> getHTTPPeakListEnclosure ( const String &  filename  )  const

enclosing Strings of the peak list body for HTTP submission

Can be used to embed custom content into HTTP submission (when writing only the MGF header in HTTP format and then adding the peaks (in whatever format, e.g. mzXML) enclosed in this body. The filename can later be found in the Mascot response.

bool getNextSpectrum_ ( std::istream &  is,
std::vector< std::pair< double, double > > &  spectrum,
UInt &  charge,
double &  precursor_mz,
double &  precursor_int,
double &  rt,
String &  title,
Size &  line_number 
) [protected]

reads a spectrum block, the section between 'BEGIN IONS' and 'END IONS' of a mgf file

void load ( const String &  filename,
MapType &  exp 
) [inline]

loads a Mascot Generic File into a PeakMap

Parameters:
filename file name which the map should be read from
exp the map which is filled with the data from the given file
Exceptions:
FileNotFound is thrown if the given file could not be found

References File::exists(), and Peak2D::setPosition().

Referenced by FileHandler::loadExperiment().

void store ( std::ostream &  os,
const String &  filename,
const PeakMap &  experiment 
)

store the experiment data in a MascotGenericFile; the output is written to the given stream, the filename will be noted in the file

void store ( const String &  filename,
const PeakMap &  experiment 
)

stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell execution

void writeHeader_ ( std::ostream &  os  )  [protected]

writes the full header

void writeMSExperiment_ ( std::ostream &  os,
const String &  filename,
const PeakMap &  experiment 
) [protected]

writes the MSExperiment

void writeParameterHeader_ ( const String &  name,
std::ostream &  os 
) [protected]

writes a parameter header

void writeSpectrum_ ( std::ostream &  os,
const PeakSpectrum &  spec,
const String &  filename 
) [protected]

writes the spectrum

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1