Class: PeptideQuantification

This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information

classDiagram class PeptideQuantification click PeptideQuantification href "../PeptideQuantification" PeptideQuantification : all_proteins PeptideQuantification --> "*" GeneProduct : all_proteins click GeneProduct href "../GeneProduct" PeptideQuantification : best_protein PeptideQuantification --> "1" GeneProduct : best_protein click GeneProduct href "../GeneProduct" PeptideQuantification : min_q_value PeptideQuantification : peptide_sequence PeptideQuantification : peptide_spectral_count PeptideQuantification : peptide_sum_masic_abundance

Slots

Name	Cardinality and Range	Description	Inheritance
all_proteins	0..* GeneProduct	the list of protein identifiers that are associated with the peptide sequence	direct
best_protein	0..1 GeneProduct	the specific protein identifier most correctly associated with the peptide se...	direct
min_q_value	0..1 Float	smallest Q-Value associated with the peptide sequence as provided by MSGFPlus...	direct
peptide_sequence	0..1 String		direct
peptide_spectral_count	0..1 Integer	sum of filter passing MS2 spectra associated with the peptide sequence within...	direct
peptide_sum_masic_abundance	0..1 Integer	combined MS1 extracted ion chromatograms derived from MS2 spectra associated ...	direct

Usages

used by	used in	type	used
MetaproteomicsAnalysisActivity	has_peptide_quantifications	range	PeptideQuantification

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:PeptideQuantification
native	nmdc:PeptideQuantification

LinkML Source

Direct

name: PeptideQuantification
description: This is used to link a metaproteomics analysis workflow to a specific
  peptide sequence and related information
from_schema: https://w3id.org/nmdc/nmdc
slots:
- all_proteins
- best_protein
- min_q_value
- peptide_sequence
- peptide_spectral_count
- peptide_sum_masic_abundance

Induced

name: PeptideQuantification
description: This is used to link a metaproteomics analysis workflow to a specific
  peptide sequence and related information
from_schema: https://w3id.org/nmdc/nmdc
attributes:
  all_proteins:
    name: all_proteins
    description: the list of protein identifiers that are associated with the peptide
      sequence
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: all_proteins
    owner: PeptideQuantification
    domain_of:
    - PeptideQuantification
    - ProteinQuantification
    range: GeneProduct
  best_protein:
    name: best_protein
    description: the specific protein identifier most correctly associated with the
      peptide sequence
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: best_protein
    owner: PeptideQuantification
    domain_of:
    - PeptideQuantification
    - ProteinQuantification
    range: GeneProduct
  min_q_value:
    name: min_q_value
    description: smallest Q-Value associated with the peptide sequence as provided
      by MSGFPlus tool
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - OBI:0001442
    rank: 1000
    alias: min_q_value
    owner: PeptideQuantification
    domain_of:
    - PeptideQuantification
    range: float
  peptide_sequence:
    name: peptide_sequence
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: peptide_sequence
    owner: PeptideQuantification
    domain_of:
    - PeptideQuantification
    range: string
  peptide_spectral_count:
    name: peptide_spectral_count
    description: sum of filter passing MS2 spectra associated with the peptide sequence
      within a given LC-MS/MS data file
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: peptide_spectral_count
    owner: PeptideQuantification
    domain_of:
    - PeptideQuantification
    range: integer
  peptide_sum_masic_abundance:
    name: peptide_sum_masic_abundance
    description: combined MS1 extracted ion chromatograms derived from MS2 spectra
      associated with the peptide sequence from a given LC-MS/MS data file using the
      MASIC tool
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: peptide_sum_masic_abundance
    owner: PeptideQuantification
    domain_of:
    - PeptideQuantification
    range: integer