Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Member Functions | Protected Member Functions | List of all members
MascotGenericFile Class Reference

Mascot input file adapter. More...

#include <OpenMS/FORMAT/MascotGenericFile.h>

Inheritance diagram for MascotGenericFile:
ProgressLogger DefaultParamHandler

Public Member Functions

 MascotGenericFile ()
 constructor More...
 
virtual ~MascotGenericFile ()
 constructor More...
 
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 More...
 
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 More...
 
template<typename MapType >
void load (const String &filename, MapType &exp)
 loads a Mascot Generic File into a PeakMap More...
 
std::pair< String, StringgetHTTPPeakListEnclosure (const String &filename) const
 enclosing Strings of the peak list body for HTTP submission More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. 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

void writeParameterHeader_ (const String &name, std::ostream &os)
 writes a parameter header More...
 
void writeHeader_ (std::ostream &os)
 writes the full header More...
 
void writeSpectrum_ (std::ostream &os, const PeakSpectrum &spec, const String &filename)
 writes the spectrum More...
 
void writeMSExperiment_ (std::ostream &os, const String &filename, const PeakMap &experiment)
 writes the MSExperiment More...
 
bool getNextSpectrum_ (std::istream &is, std::vector< std::pair< String, String > > &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 More...
 
- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 
- 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...
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

Mascot input file adapter.

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

Loading a file supports multi-threading, since conversion from string to double is expensive and takes long using a single thread.

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.
email string  Sets the email which is mentioned in the results file. Note: Some server require that a proper email is provided.
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

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< String, String > > &  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
filenamefile name which the map should be read from
expthe map which is filled with the data from the given file
Exceptions
FileNotFoundis thrown if the given file could not be found

References File::exists().

Referenced by FileHandler::loadExperiment().

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

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 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5