OpenMS::Constants::UserParam Namespace Reference

Variables
const std::string	CONCAT_PEPTIDE
const std::string	LOCALIZED_MODIFICATIONS_USERPARAM
const std::string	MERGED_CHROMATOGRAM_MZS
const std::string	PRECURSOR_ERROR_PPM_USERPARAM
const std::string	FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM
const std::string	FRAGMENT_ANNOTATION_USERPARAM
const std::string	SPECTRUM_REFERENCE
const std::string	TARGET_DECOY
const std::string	DELTA_SCORE
const std::string	ISOTOPE_ERROR
const std::string	OPENPEPXL_SCORE
const std::string	OPENPEPXL_BETA_SEQUENCE
const std::string	OPENPEPXL_BETA_ACCESSIONS
const std::string	OPENPEPXL_XL_POS1
const std::string	OPENPEPXL_XL_POS2
const std::string	OPENPEPXL_XL_POS1_PROT
const std::string	OPENPEPXL_XL_POS2_PROT
const std::string	OPENPEPXL_XL_TYPE
const std::string	OPENPEPXL_XL_RANK
const std::string	OPENPEPXL_XL_MOD
const std::string	OPENPEPXL_XL_MASS
const std::string	OPENPEPXL_XL_TERM_SPEC_ALPHA
const std::string	OPENPEPXL_XL_TERM_SPEC_BETA
const std::string	OPENPEPXL_HEAVY_SPEC_RT
const std::string	OPENPEPXL_HEAVY_SPEC_MZ
const std::string	OPENPEPXL_HEAVY_SPEC_REF
const std::string	OPENPEPXL_TARGET_DECOY_ALPHA
const std::string	OPENPEPXL_TARGET_DECOY_BETA
const std::string	OPENPEPXL_BETA_PEPEV_PRE
const std::string	OPENPEPXL_BETA_PEPEV_POST
const std::string	OPENPEPXL_BETA_PEPEV_START
const std::string	OPENPEPXL_BETA_PEPEV_END
const std::string	XFDR_FDR

Variable Documentation

CONCAT_PEPTIDE

const std::string CONCAT_PEPTIDE

User parameter name for identifier of concatenated peptides String

DELTA_SCORE

const std::string DELTA_SCORE

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

User parameter name for fragment annotations String

FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM

const std::string FRAGMENT_ERROR_MEDIAN_PPM_USERPARAM

User parameter name for fragment mz error in ppm String

ISOTOPE_ERROR

const std::string ISOTOPE_ERROR

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

Metavalue to list unimod modifications used in site localization

MERGED_CHROMATOGRAM_MZS

const std::string MERGED_CHROMATOGRAM_MZS

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

OPENPEPXL_BETA_ACCESSIONS

const std::string OPENPEPXL_BETA_ACCESSIONS

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

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

OPENPEPXL_BETA_PEPEV_POST

const std::string OPENPEPXL_BETA_PEPEV_POST

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

OPENPEPXL_BETA_PEPEV_PRE

const std::string OPENPEPXL_BETA_PEPEV_PRE

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

OPENPEPXL_BETA_PEPEV_START

const std::string OPENPEPXL_BETA_PEPEV_START

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

OPENPEPXL_BETA_SEQUENCE

const std::string OPENPEPXL_BETA_SEQUENCE

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

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

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

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

Name of OpenPepXL main score (PSI CV term) String

OPENPEPXL_TARGET_DECOY_ALPHA

const std::string OPENPEPXL_TARGET_DECOY_ALPHA

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

OPENPEPXL_TARGET_DECOY_BETA

const std::string OPENPEPXL_TARGET_DECOY_BETA

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

OPENPEPXL_XL_MASS

const std::string OPENPEPXL_XL_MASS

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

OPENPEPXL_XL_MOD

const std::string OPENPEPXL_XL_MOD

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

OPENPEPXL_XL_POS1

const std::string OPENPEPXL_XL_POS1

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

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

OPENPEPXL_XL_POS2

const std::string OPENPEPXL_XL_POS2

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

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

OPENPEPXL_XL_RANK

const std::string OPENPEPXL_XL_RANK

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

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

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

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

User parameter name for precursor mz error in ppm String

Referenced by NucleicAcidSearchEngine::postProcessHits_().

SPECTRUM_REFERENCE

const std::string SPECTRUM_REFERENCE

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

TARGET_DECOY

const std::string TARGET_DECOY

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

User parameter name for XL-MS FDR values String