OpenMS
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Variables | |
const std::string | CONCAT_PEPTIDE = "concatenated_peptides" |
const std::string | LOCALIZED_MODIFICATIONS_USERPARAM = "localized_modifications" |
const std::string | MERGED_CHROMATOGRAM_MZS = "merged_chromatogram_mzs" |
const std::string | PRECURSOR_ERROR_PPM_USERPARAM = "precursor_mz_error_ppm" |
const std::string | FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM = "fragment_mz_error_median_ppm" |
const std::string | FRAGMENT_ERROR_PPM_USERPARAM = "fragment_mass_error_ppm" |
const std::string | FRAGMENT_ERROR_DA_USERPARAM = "fragment_mass_error_da" |
const std::string | FRAGMENT_ANNOTATION_USERPARAM = "fragment_annotation" |
const std::string | PSM_EXPLAINED_ION_CURRENT_USERPARAM = "PSM_explained_ion_current" |
const std::string | MATCHED_PREFIX_IONS_FRACTION = "matched_prefix_ions_fraction" |
const std::string | MATCHED_SUFFIX_IONS_FRACTION = "matched_suffix_ions_fraction" |
const std::string | SPECTRUM_REFERENCE = "spectrum_reference" |
const std::string | ID_MERGE_INDEX = "id_merge_index" |
const std::string | TARGET_DECOY = "target_decoy" |
const std::string | DELTA_SCORE = "delta_score" |
const std::string | ISOTOPE_ERROR = "isotope_error" |
const std::string | OPENPEPXL_SCORE = "OpenPepXL:score" |
const std::string | OPENPEPXL_BETA_SEQUENCE = "sequence_beta" |
const std::string | OPENPEPXL_BETA_ACCESSIONS = "accessions_beta" |
const std::string | OPENPEPXL_XL_POS1 = "xl_pos1" |
const std::string | OPENPEPXL_XL_POS2 = "xl_pos2" |
const std::string | OPENPEPXL_XL_POS1_PROT = "xl_pos1_protein" |
const std::string | OPENPEPXL_XL_POS2_PROT = "xl_pos2_protein" |
const std::string | OPENPEPXL_XL_TYPE = "xl_type" |
const std::string | OPENPEPXL_XL_RANK = "xl_rank" |
const std::string | OPENPEPXL_XL_MOD = "xl_mod" |
const std::string | OPENPEPXL_XL_MASS = "xl_mass" |
const std::string | OPENPEPXL_XL_TERM_SPEC_ALPHA = "xl_term_spec_alpha" |
const std::string | OPENPEPXL_XL_TERM_SPEC_BETA = "xl_term_spec_beta" |
const std::string | OPENPEPXL_HEAVY_SPEC_RT = "spec_heavy_RT" |
const std::string | OPENPEPXL_HEAVY_SPEC_MZ = "spec_heavy_MZ" |
const std::string | OPENPEPXL_HEAVY_SPEC_REF = "spectrum_reference_heavy" |
const std::string | OPENPEPXL_TARGET_DECOY_ALPHA = "xl_target_decoy_alpha" |
const std::string | OPENPEPXL_TARGET_DECOY_BETA = "xl_target_decoy_beta" |
const std::string | OPENPEPXL_BETA_PEPEV_PRE = "BetaPepEv:pre" |
const std::string | OPENPEPXL_BETA_PEPEV_POST = "BetaPepEv:post" |
const std::string | OPENPEPXL_BETA_PEPEV_START = "BetaPepEv:start" |
const std::string | OPENPEPXL_BETA_PEPEV_END = "BetaPepEv:end" |
const std::string | XFDR_FDR = "XFDR:FDR" |
const std::string | IIMN_BEST_ION = "best ion" |
const std::string | IIMN_ADDUCT_PARTNERS = "partners" |
const std::string | IIMN_ROW_ID = "row ID" |
const std::string | IIMN_ANNOTATION_NETWORK_NUMBER = "annotation network number" |
const std::string | ADDUCT_GROUP = "Group" |
const std::string | IIMN_LINKED_GROUPS = "LinkedGroups" |
const std::string | DC_CHARGE_ADDUCTS = "dc_charge_adducts" |
const std::string | NUM_OF_MASSTRACES = "num_of_masstraces" |
const std::string | NUM_OF_DATAPOINTS = "num_of_datapoints" |
const std::string | MSM_METABOLITE_NAME = "Metabolite_Name" |
const std::string | MSM_INCHI_STRING = "Inchi_String" |
const std::string | MSM_SMILES_STRING = "SMILES_String" |
const std::string | MSM_PRECURSOR_ADDUCT = "Precursor_Ion" |
const std::string | MSM_SUM_FORMULA = "Sum_Formula" |
User parameters in/from Sirius annotated mzMLs | |
E.g., when running SiriusAdapter with annotation output | |
const std::string | SIRIUS_MZ = "mz" |
const std::string | SIRIUS_EXACTMASS = "exact_mass" |
const std::string | SIRIUS_EXPLANATION = "explanation" |
const std::string | SIRIUS_SCORE = "score" |
const std::string | SIRIUS_PEAKMZ = "peak_mz" |
const std::string | SIRIUS_ANNOTATED_SUMFORMULA = "annotated_sumformula" |
const std::string | SIRIUS_ANNOTATED_ADDUCT = "annotated_adduct" |
const std::string | SIRIUS_DECOY = "decoy" |
const std::string | SIRIUS_FEATURE_ID = "feat_id" |
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User parameter name for identifier of concatenated peptides String
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User parameter name for a delta score: a score ratio between a rank x hit and the rank x+1 hit String
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User parameter name for fragment annotations String
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User parameter name for fragment mz error in dalton String
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User parameter name for median of fragment mz error in ppm String
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User parameter name for fragment mz error in ppm String
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User parameter name to store the index of the primary MS run associated with the PeptideIdentification (it is not yet treated as a class attribute). Set by IDMerger algorithm or when reading ID files with info from multiple files (e.g., PercolatorInfile) String
Referenced by ProteinIdentification::Mapping::getPrimaryMSRunPath().
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User parameter name for a ConsensusFeature. Represents the IIMN_ROW_IDs of related ConsensusFeatures defined by MetaboliteAdductDecharger. Partners are separated by semin colon. (Required for IIMN) List of String
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User parameter name for a ConsensusFeature to indicate a metabolite with different adduct states. (Required for IIMN) String
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User parameter name for best ion annotation in a ConsensusFeature, taken from the best quality feature. (Required for IIMN) String
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User parameter name for a list of ADDUCT_GROUP annotations in a ConsensusFeature. (Required for IIMN) vector<String>
Referenced by TOPPGNPSExport::main_().
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User parameter name for a unique ConsensusFeature index in a ConsensusMap. (Required for IIMN) String
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User parameter name to indicate a monoisotopic peak misassignment. Used for precursor correction. (usually an integer x with the correction being -x times C13C12_MASSDIFF_U) String
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Metavalue to list unimod modifications used in site localization
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User parameter name for the M/Z of other chromatograms which have been merged into this one String
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User parameter name for the INCHI key associated with a metabolite. (Required for MetaboliteSpectralMatcher) String
Referenced by MascotGenericFile::getNextSpectrum_().
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User parameter name for the name/description of a metabolite. (Required for MetaboliteSpectralMatcher) String
Referenced by MascotGenericFile::getNextSpectrum_().
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User parameter name for the precursor adduct ion of a metabolite. (Required for MetaboliteSpectralMatcher) String
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User parameter name for the SMILES key associated with a metabolite. (Required for MetaboliteSpectralMatcher) String
Referenced by MascotGenericFile::getNextSpectrum_().
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User parameter name for the sum formula of a metabolite. (Required for MetaboliteSpectralMatcher) String
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User parameter name for the total number of data points (peaks) in a feature. (Required for MQEvidenceExporter) String
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User parameter name for the number of mass traces in a feature. (Required for SiriusAdapter) String
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User parameter name for the protein accessions of the second peptide in a cross-link String
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User parameter name for PeptideEvidence info for the beta/acceptor peptide: end String
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User parameter name for PeptideEvidence info for the beta/acceptor peptide: post String
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User parameter name for PeptideEvidence info for the beta/acceptor peptide: pre String
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User parameter name for PeptideEvidence info for the beta/acceptor peptide: start String
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User parameter name for the sequence of the second peptide in a cross-link String
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User parameter name for the m/z of the heavy spectrum precursor in a labeled cross-linking experiment String
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User parameter name for the spectrum reference of the heavy spectrum in a labeled cross-linking experiment String
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User parameter name for the RT of the heavy spectrum precursor in a labeled cross-linking experiment String
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Name of OpenPepXL main score (PSI CV term) String
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User parameter name for target/decoy annotation of alpha peptides String
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User parameter name for target/decoy annotation of beta peptides String
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User parameter name for the mass of a cross-link String
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User parameter name for the name of a cross-link String
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User parameter name for the 1st position of cross-link (alpha peptide position in a real cross-link, 1st of two positions in a loop-link, modified position in a mono-link) String
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User parameter name for the 1st cross-link position on the protein String
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User parameter name for the 2nd position of cross-link (beta peptide position in a real cross-link, 2nd of two positions in a loop-link, "-" in a mono-link) String
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User parameter name for the 2nd cross-link position on the protein String
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User parameter name for the cross-link rank (ranks of PeptideHits across different PeptideIdentifications) String
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User parameter name for the terminal specificity of a cross-link on the alpha peptide (to distinguish a link to the first or last residue side chain from a terminal link) String
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User parameter name for the terminal specificity of a cross-link on the beta peptide (to distinguish a link to the first or last residue side chain from a terminal link) String
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User parameter name for the cross-link type, one of: cross-link, loop-link, mono-link String
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User parameter name for precursor mz error in ppm String
Referenced by NucleicAcidSearchEngine::postProcessHits_().
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User parameter name for annotation of PSMExlpainedIonCurrent String
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User parameter name to tell which adduct was considered for this annotated spectrum String
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User parameter name to tell which sum formula was considered for this annotated spectrum String
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User parameter name to tell if this annotated spectrum comes from a Sirius/Passatutto generated decoy or an actual target spectrum boolean
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FloatDataArray name for exact mass values of Sirius annotated spectra FloatDataArray
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StringDataArray name for most likely fragment explanations of the corresponding peak in the spectrum StringDataArray
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User parameter name to tell if this annotated spectrum comes from a feature (then it contains the feature ID) or a single MS2 spectrum (missing) boolean
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FloatDataArray name for observed m/z values of Sirius annotated spectra FloatDataArray
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User parameter name to tell what the contents of the m/z dimension of the annotated spectra contains (mz or exact mass) String
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User parameter name for Sirius score double
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User parameter name for the spectrum reference in PeptideIdentification (it is not yet treated as a class attribute) String
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User parameter name for target/decoy annotation of a PeptideHit, e.g. as annotated by PeptideIndexer. One of: target, decoy, target+decoy String
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User parameter name for XL-MS FDR values String