Identifies peptides in MS/MS spectra via OMSSA (Open Mass Spectrometry Search Algorithm).
Sequence databases in FASTA format must be converted into the NCBI format before OMSSA can read them. For this, you can use the program 'formatdb' (old releases) or 'makeblastdb' (recent release) of the NCBI-tools suite, which is freely available for download. Use formatdb -i SwissProt_TargetAndDecoy.fasta -o to create a BLAST database, which actually consists of multiple files. The more recent 'makeblastdb' has a similar syntax, e.g., makeblastdb -dbtype prot -in SwissProt_TargetAndDecoy.fasta .
Make sure that your FASTA file (which you convert into BLAST database files) is properly formatted, especially that it conforms to the FASTA Defline format and that there is a description(!), i.e. '>ID DESCRIPTION'. Otherwise you might get a
As database parameter for the OMSSAAdapter you can either specify the .psq file as generated by formatdb/makeblastdb (e.g., 'SwissProt_TargetAndDecoy.fasta.psq') or the original FASTA file (e.g., 'SwissProt_TargetAndDecoy.fasta'). This makes it easy to specify a common TOPPAS input node (using only the FASTA suffix) for many adapters. Just make sure that the .psq and .fasta file reside in the same directory!
This adapter supports relative database filenames, which (when not found in the current working directory) is looked up in the directories specified by 'OpenMS.ini:id_db_dir' (see TOPP for Advanced Users).
This wrapper has been tested successfully with OMSSA, version 2.x.
Legend:
 required parameter
 advanced parameter
 
  +OMSSAAdapterAnnotates MS/MS spectra using OMSSA.
    version1.11.1
Version of the tool that generated this parameters file. 
    ++1Instance '1' section for 'OMSSAAdapter'
      in
Input file input file*.mzML
      out
Output file output file*.idXML
      precursor_mass_tolerance1.5
Precursor mass tolerance (Default: Dalton) 
      precursor_mass_tolerance_unit_ppmfalse
If this flag is set, ppm is used as precursor mass tolerance unittrue,false
      fragment_mass_tolerance0.3
Fragment mass error in Dalton 
      database
NCBI formatted FASTA files. Only the .psq filename should be given, e.g. 'SwissProt.fasta.psq'. If the filename does not end in '.psq' the suffix will be added automatically. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'input file*.psq,*.fasta
      min_precursor_charge1
Minimum precursor ion charge 
      max_precursor_charge3
Maximum precursor ion charge 
      fixed_modifications[]
Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'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[]
Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'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)
      omssa_executableomssacl
The 'omssacl' executable of the OMSSA installationinput file 
      pc1
The number of pseudocounts to add to each precursor mass bin 
      hs4
the minimum number of m/z values a spectrum must have to be searched 
      tez1
scaling of precursor mass tolerance with charge (0 = none, 1= linear) 
      tom0
product ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact 
      tem0
precursor ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact 
      tex1446.94
threshold in Da above which the mass of a neutron should be added in an exact mass search 
      zt3
minimum precursor charge to start considering multiply charged products 
      z10.95
the fraction of peaks below the precursor used to determine if the spectrum is charge +1 
      zc1
should charge +1 be determined algorithmically (1=yes) 
      zcc2
how should precursor charges be determined? (1=believe the input file,2=use the specified range) 
      zoh2
set the maximum product charge to search 
      v1
number of missed cleavages allowed 
      e0
id number of enzyme to use (0 (i.e. trypsin) is the default, 17 would be no enzyme (i.e. unspecific digestion), for more please refer to omssacl -help). 
      no4
minimum size of peptides for no-enzyme and semi-tryptic searches 
      nox40
maximum size of peptides for no-enzyme and semi-tryptic searches 
      i1,4
comma delimited list of id numbers of ions to search 
      sp100
number of product ions to search 
      sb11
should first forward (e.g. b1) product ions be searched (1 = no, 0 = yes) 
      sct0
should c terminus ions (e.g. y1) be searched (1 = no, 0 = yes) 
      x0
comma delimited list of NCBI taxonomy ids to search (0 = all.  This is the default) 
      hm2
the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded 
      ht6
number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide 
      hl30
maximum number of hits retained for one spectrum. Note: even when set to 1 OMSSA may report multiple hits with different charge states 
      he1000
the maximum e-value allowed in the hit list. If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported. 
      mm128
the maximum number of mass ladders to generate per database peptide 
      mnmfalse
n-term methionine should not be cleavedtrue,false
      is0
evalue threshold to include a sequence in the iterative search, 0 = all 
      ir0
evalue threshold to replace a hit, 0 = only if better 
      ii0
evalue threshold to iteratively search a spectrum again, 0 = always 
      log
Name of log file (created only when specified) 
      debug0
Sets the debug level 
      threads1
Sets the number of threads allowed to be used by the TOPP tool 
      no_progressfalse
Disables progress logging to command linetrue,false
      testfalse
Enables the test mode (needed for internal use only)true,false