OpenMS
Variables
OpenMS::Constants::UserParam Namespace Reference

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"
 

Variable Documentation

◆ ADDUCT_GROUP

const std::string ADDUCT_GROUP = "Group"
inline

User parameter name for group annotation in Feature by MetaboliteAdductDecharger to indicate matching Features with different adducts. String

◆ CONCAT_PEPTIDE

const std::string CONCAT_PEPTIDE = "concatenated_peptides"
inline

User parameter name for identifier of concatenated peptides String

◆ DC_CHARGE_ADDUCTS

const std::string DC_CHARGE_ADDUCTS = "dc_charge_adducts"
inline

User parameter name for adduct annotation in Feature by MetaboliteAdductDecharger. String

◆ DELTA_SCORE

const std::string DELTA_SCORE = "delta_score"
inline

User parameter name for a delta score: a score ratio between a rank x hit and the rank x+1 hit String

◆ FRAGMENT_ANNOTATION_USERPARAM

const std::string FRAGMENT_ANNOTATION_USERPARAM = "fragment_annotation"
inline

User parameter name for fragment annotations String

◆ FRAGMENT_ERROR_DA_USERPARAM

const std::string FRAGMENT_ERROR_DA_USERPARAM = "fragment_mass_error_da"
inline

User parameter name for fragment mz error in dalton String

◆ FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM

const std::string FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM = "fragment_mz_error_median_ppm"
inline

User parameter name for median of fragment mz error in ppm String

◆ FRAGMENT_ERROR_PPM_USERPARAM

const std::string FRAGMENT_ERROR_PPM_USERPARAM = "fragment_mass_error_ppm"
inline

User parameter name for fragment mz error in ppm String

◆ ID_MERGE_INDEX

const std::string ID_MERGE_INDEX = "id_merge_index"
inline

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().

◆ IIMN_ADDUCT_PARTNERS

const std::string IIMN_ADDUCT_PARTNERS = "partners"
inline

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

◆ IIMN_ANNOTATION_NETWORK_NUMBER

const std::string IIMN_ANNOTATION_NETWORK_NUMBER = "annotation network number"
inline

User parameter name for a ConsensusFeature to indicate a metabolite with different adduct states. (Required for IIMN) String

◆ IIMN_BEST_ION

const std::string IIMN_BEST_ION = "best ion"
inline

User parameter name for best ion annotation in a ConsensusFeature, taken from the best quality feature. (Required for IIMN) String

◆ IIMN_LINKED_GROUPS

const std::string IIMN_LINKED_GROUPS = "LinkedGroups"
inline

User parameter name for a list of ADDUCT_GROUP annotations in a ConsensusFeature. (Required for IIMN) vector<String>

Referenced by TOPPGNPSExport::main_().

◆ IIMN_ROW_ID

const std::string IIMN_ROW_ID = "row ID"
inline

User parameter name for a unique ConsensusFeature index in a ConsensusMap. (Required for IIMN) String

◆ ISOTOPE_ERROR

const std::string ISOTOPE_ERROR = "isotope_error"
inline

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

◆ LOCALIZED_MODIFICATIONS_USERPARAM

const std::string LOCALIZED_MODIFICATIONS_USERPARAM = "localized_modifications"
inline

Metavalue to list unimod modifications used in site localization

◆ MATCHED_PREFIX_IONS_FRACTION

const std::string MATCHED_PREFIX_IONS_FRACTION = "matched_prefix_ions_fraction"
inline

◆ MATCHED_SUFFIX_IONS_FRACTION

const std::string MATCHED_SUFFIX_IONS_FRACTION = "matched_suffix_ions_fraction"
inline

◆ MERGED_CHROMATOGRAM_MZS

const std::string MERGED_CHROMATOGRAM_MZS = "merged_chromatogram_mzs"
inline

User parameter name for the M/Z of other chromatograms which have been merged into this one String

◆ MSM_INCHI_STRING

const std::string MSM_INCHI_STRING = "Inchi_String"
inline

User parameter name for the INCHI key associated with a metabolite. (Required for MetaboliteSpectralMatcher) String

Referenced by MascotGenericFile::getNextSpectrum_().

◆ MSM_METABOLITE_NAME

const std::string MSM_METABOLITE_NAME = "Metabolite_Name"
inline

User parameter name for the name/description of a metabolite. (Required for MetaboliteSpectralMatcher) String

Referenced by MascotGenericFile::getNextSpectrum_().

◆ MSM_PRECURSOR_ADDUCT

const std::string MSM_PRECURSOR_ADDUCT = "Precursor_Ion"
inline

User parameter name for the precursor adduct ion of a metabolite. (Required for MetaboliteSpectralMatcher) String

◆ MSM_SMILES_STRING

const std::string MSM_SMILES_STRING = "SMILES_String"
inline

User parameter name for the SMILES key associated with a metabolite. (Required for MetaboliteSpectralMatcher) String

Referenced by MascotGenericFile::getNextSpectrum_().

◆ MSM_SUM_FORMULA

const std::string MSM_SUM_FORMULA = "Sum_Formula"
inline

User parameter name for the sum formula of a metabolite. (Required for MetaboliteSpectralMatcher) String

◆ NUM_OF_DATAPOINTS

const std::string NUM_OF_DATAPOINTS = "num_of_datapoints"
inline

User parameter name for the total number of data points (peaks) in a feature. (Required for MQEvidenceExporter) String

◆ NUM_OF_MASSTRACES

const std::string NUM_OF_MASSTRACES = "num_of_masstraces"
inline

User parameter name for the number of mass traces in a feature. (Required for SiriusAdapter) String

◆ OPENPEPXL_BETA_ACCESSIONS

const std::string OPENPEPXL_BETA_ACCESSIONS = "accessions_beta"
inline

User parameter name for the protein accessions of the second peptide in a cross-link String

◆ OPENPEPXL_BETA_PEPEV_END

const std::string OPENPEPXL_BETA_PEPEV_END = "BetaPepEv:end"
inline

User parameter name for PeptideEvidence info for the beta/acceptor peptide: end String

◆ OPENPEPXL_BETA_PEPEV_POST

const std::string OPENPEPXL_BETA_PEPEV_POST = "BetaPepEv:post"
inline

User parameter name for PeptideEvidence info for the beta/acceptor peptide: post String

◆ OPENPEPXL_BETA_PEPEV_PRE

const std::string OPENPEPXL_BETA_PEPEV_PRE = "BetaPepEv:pre"
inline

User parameter name for PeptideEvidence info for the beta/acceptor peptide: pre String

◆ OPENPEPXL_BETA_PEPEV_START

const std::string OPENPEPXL_BETA_PEPEV_START = "BetaPepEv:start"
inline

User parameter name for PeptideEvidence info for the beta/acceptor peptide: start String

◆ OPENPEPXL_BETA_SEQUENCE

const std::string OPENPEPXL_BETA_SEQUENCE = "sequence_beta"
inline

User parameter name for the sequence of the second peptide in a cross-link String

◆ OPENPEPXL_HEAVY_SPEC_MZ

const std::string OPENPEPXL_HEAVY_SPEC_MZ = "spec_heavy_MZ"
inline

User parameter name for the m/z of the heavy spectrum precursor in a labeled cross-linking experiment String

◆ OPENPEPXL_HEAVY_SPEC_REF

const std::string OPENPEPXL_HEAVY_SPEC_REF = "spectrum_reference_heavy"
inline

User parameter name for the spectrum reference of the heavy spectrum in a labeled cross-linking experiment String

◆ OPENPEPXL_HEAVY_SPEC_RT

const std::string OPENPEPXL_HEAVY_SPEC_RT = "spec_heavy_RT"
inline

User parameter name for the RT of the heavy spectrum precursor in a labeled cross-linking experiment String

◆ OPENPEPXL_SCORE

const std::string OPENPEPXL_SCORE = "OpenPepXL:score"
inline

Name of OpenPepXL main score (PSI CV term) String

◆ OPENPEPXL_TARGET_DECOY_ALPHA

const std::string OPENPEPXL_TARGET_DECOY_ALPHA = "xl_target_decoy_alpha"
inline

User parameter name for target/decoy annotation of alpha peptides String

◆ OPENPEPXL_TARGET_DECOY_BETA

const std::string OPENPEPXL_TARGET_DECOY_BETA = "xl_target_decoy_beta"
inline

User parameter name for target/decoy annotation of beta peptides String

◆ OPENPEPXL_XL_MASS

const std::string OPENPEPXL_XL_MASS = "xl_mass"
inline

User parameter name for the mass of a cross-link String

◆ OPENPEPXL_XL_MOD

const std::string OPENPEPXL_XL_MOD = "xl_mod"
inline

User parameter name for the name of a cross-link String

◆ OPENPEPXL_XL_POS1

const std::string OPENPEPXL_XL_POS1 = "xl_pos1"
inline

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

◆ OPENPEPXL_XL_POS1_PROT

const std::string OPENPEPXL_XL_POS1_PROT = "xl_pos1_protein"
inline

User parameter name for the 1st cross-link position on the protein String

◆ OPENPEPXL_XL_POS2

const std::string OPENPEPXL_XL_POS2 = "xl_pos2"
inline

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

◆ OPENPEPXL_XL_POS2_PROT

const std::string OPENPEPXL_XL_POS2_PROT = "xl_pos2_protein"
inline

User parameter name for the 2nd cross-link position on the protein String

◆ OPENPEPXL_XL_RANK

const std::string OPENPEPXL_XL_RANK = "xl_rank"
inline

User parameter name for the cross-link rank (ranks of PeptideHits across different PeptideIdentifications) String

◆ OPENPEPXL_XL_TERM_SPEC_ALPHA

const std::string OPENPEPXL_XL_TERM_SPEC_ALPHA = "xl_term_spec_alpha"
inline

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

◆ OPENPEPXL_XL_TERM_SPEC_BETA

const std::string OPENPEPXL_XL_TERM_SPEC_BETA = "xl_term_spec_beta"
inline

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

◆ OPENPEPXL_XL_TYPE

const std::string OPENPEPXL_XL_TYPE = "xl_type"
inline

User parameter name for the cross-link type, one of: cross-link, loop-link, mono-link String

◆ PRECURSOR_ERROR_PPM_USERPARAM

const std::string PRECURSOR_ERROR_PPM_USERPARAM = "precursor_mz_error_ppm"
inline

User parameter name for precursor mz error in ppm String

Referenced by NucleicAcidSearchEngine::postProcessHits_().

◆ PSM_EXPLAINED_ION_CURRENT_USERPARAM

const std::string PSM_EXPLAINED_ION_CURRENT_USERPARAM = "PSM_explained_ion_current"
inline

User parameter name for annotation of PSMExlpainedIonCurrent String

◆ SIRIUS_ANNOTATED_ADDUCT

const std::string SIRIUS_ANNOTATED_ADDUCT = "annotated_adduct"
inline

User parameter name to tell which adduct was considered for this annotated spectrum String

◆ SIRIUS_ANNOTATED_SUMFORMULA

const std::string SIRIUS_ANNOTATED_SUMFORMULA = "annotated_sumformula"
inline

User parameter name to tell which sum formula was considered for this annotated spectrum String

◆ SIRIUS_DECOY

const std::string SIRIUS_DECOY = "decoy"
inline

User parameter name to tell if this annotated spectrum comes from a Sirius/Passatutto generated decoy or an actual target spectrum boolean

◆ SIRIUS_EXACTMASS

const std::string SIRIUS_EXACTMASS = "exact_mass"
inline

FloatDataArray name for exact mass values of Sirius annotated spectra FloatDataArray

◆ SIRIUS_EXPLANATION

const std::string SIRIUS_EXPLANATION = "explanation"
inline

StringDataArray name for most likely fragment explanations of the corresponding peak in the spectrum StringDataArray

◆ SIRIUS_FEATURE_ID

const std::string SIRIUS_FEATURE_ID = "feat_id"
inline

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

◆ SIRIUS_MZ

const std::string SIRIUS_MZ = "mz"
inline

FloatDataArray name for observed m/z values of Sirius annotated spectra FloatDataArray

◆ SIRIUS_PEAKMZ

const std::string SIRIUS_PEAKMZ = "peak_mz"
inline

User parameter name to tell what the contents of the m/z dimension of the annotated spectra contains (mz or exact mass) String

◆ SIRIUS_SCORE

const std::string SIRIUS_SCORE = "score"
inline

User parameter name for Sirius score double

◆ SPECTRUM_REFERENCE

const std::string SPECTRUM_REFERENCE = "spectrum_reference"
inline

User parameter name for the spectrum reference in PeptideIdentification (it is not yet treated as a class attribute) String

◆ TARGET_DECOY

const std::string TARGET_DECOY = "target_decoy"
inline

User parameter name for target/decoy annotation of a PeptideHit, e.g. as annotated by PeptideIndexer. One of: target, decoy, target+decoy String

◆ XFDR_FDR

const std::string XFDR_FDR = "XFDR:FDR"
inline

User parameter name for XL-MS FDR values String