Bundled CV terms for TDAuditor #324
Description
Individual term requests are combined here after an initial discussion, to simplify porting them over to the PSI-MS CV.
Proposed CV terms:
[Term]
id: MS:1000XXX
name: TDAuditor
def: "TDAuditor is software for characterizing top-down proteome data and its deconvolutions, based on paired mzML and msAlign files." [PSI:MS, https://github.com/dtabb73/TDAuditor]
is_a: MS:1001456 ! analysis software
[Term]
id: MS:4000XXX
name: count of deconvolved MSn spectra
def: "The number of MSn spectra that produced at least one deconvolved neutral mass in a given run. Higher counts indicate a larger fraction of interpretable MSn spectra." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! higher is better
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MSn spectra without deconvolved masses
def: "The number of MSn spectra in a run that did not produce any deconvolved neutral masses, either because the MSn was excluded from the output or because the deconvolution process yielded zero masses." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! lower is better
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: fraction of similar MSn spectrum pairs
def: "The fraction of pairwise MSn spectrum comparisons that meet the similarity criterion based on shared deconvolved neutral masses." [PSI:MS]
comment: "Each MSn spectrum containing at least one deconvolved mass is compared to every other such spectrum. A pair is considered similar when their deconvolved mass profiles overlap sufficiently according to the applied similarity criterion. The metric is the number of similar pairs divided by the total number of pairs compared."
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000191 ! fraction
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: maximum similarity degree among MSn spectra
def: "The maximum number of similarity links connecting a single MSn spectrum to other MSn spectra within the similarity graph constructed from shared deconvolved neutral masses." [PSI:MS]
comment: "Each MSn spectrum is represented as a node in a similarity graph where edges denote spectral similarity based on shared deconvolved masses. This metric reports the highest node degree observed, indicating the most connected spectrum in the run. A higher value suggests one or more spectra are highly similar to many others, reflecting either redundancy or strong motif repetition."
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: size of largest connected component among MSn spectra
def: "The number of MSn spectra contained in the largest connected component of the MSn spectral similarity graph, where edges denote similarity between deconvolved spectra based on shared neutral masses." [PSI:MS]
comment: "Each MSn spectrum containing at least one deconvolved mass is represented as a node in a similarity graph. Spectra connected by similarity edges form connected components. This metric reports the membership count of the largest connected component, reflecting the most extensive group of mutually related spectra within the run."
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: number of connected components among MSn spectra
def: "The number of connected components in the MSn spectral similarity graph, where each connected component consists of MSn spectra that are all directly or indirectly similar to each other based on shared deconvolved neutral masses." [PSI:MS]
comment: "Each MSn spectrum containing at least one deconvolved mass is represented as a node in a similarity graph. Edges denote spectral similarity, and connected components represent disjoint groups of mutually related spectra. This metric reports how many such components exist within a run, reflecting the overall fragmentation or clustering of the similarity graph."
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MSn spectra acquired with HCD
def: "The number of MSn spectra in a run that report the use of higher-energy collisional dissociation (HCD) as the sole activation method." [PSI:MS]
is_a: MS:4000XXX ! fragmentation efficiency metric
relationship: part_of_workflow_stage MS:4000XXX ! mass spectrometry acquisition stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MSn spectra acquired with CID
def: "The number of MSn spectra in a run that report the use of collision-induced dissociation (CID) as the sole activation method." [PSI:MS]
is_a: MS:4000XXX ! fragmentation efficiency metric
relationship: part_of_workflow_stage MS:4000XXX ! mass spectrometry acquisition stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MSn spectra acquired with ETD
def: "The number of MSn spectra in a run that report the use of electron transfer dissociation (ETD) as the sole activation method." [PSI:MS]
is_a: MS:4000XXX ! fragmentation efficiency metric
relationship: part_of_workflow_stage MS:4000XXX ! mass spectrometry acquisition stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MSn spectra acquired with ECD
def: "The number of MSn spectra in a run that report the use of electron capture dissociation (ECD) as the sole activation method." [PSI:MS]
is_a: MS:4000XXX ! fragmentation efficiency metric
relationship: part_of_workflow_stage MS:4000XXX ! mass spectrometry acquisition stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:4000XXX ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MSn spectra acquired with EThcD
def: "The number of MSn spectra in a run that report the use of electron-transfer/higher-energy collision dissociation (EThcD) as the sole activation method." [PSI:MS]
is_a: MS:4000XXX ! fragmentation efficiency metric
relationship: part_of_workflow_stage MS:4000XXX ! mass spectrometry acquisition stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MSn spectra acquired with ETciD
def: "The number of MSn spectra in a run that report the use of electron-transfer/collision-induced dissociation (ETciD) as the sole activation method." [PSI:MS]
is_a: MS:4000XXX ! fragmentation efficiency metric
relationship: part_of_workflow_stage MS:4000XXX ! mass spectrometry acquisition stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: MS2 precursor charge quantiles
def: "Quantiles of precursor charge states reported by the instrument control software for MS2 spectra within a run. The number of values in the tuple determines the quantile mode (minimum and maximum inclusive)." [PSI:MS]
is_a: MS:4000XXX ! ionization quality metric
relationship: part_of_workflow_stage MS:4000XXX ! mass spectrometry acquisition stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! tuple
relationship: has_value_concept STATO:0000291 ! quantile
relationship: has_units MS:1000041 ! charge state
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: MS2 precursor charge quantiles from deconvolution
def: "Quantiles of precursor charge states inferred by deconvolution software for MS2 spectra within a run. The number of values in the tuple determines the quantile mode (minimum and maximum inclusive)." [PSI:MS]
is_a: MS:4000XXX ! ionization quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! tuple
relationship: has_value_concept STATO:0000291 ! quantile
relationship: has_units MS:1000041 ! charge state
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: MS2 precursor mass quantiles from deconvolution
def: "Quantiles of precursor ion masses inferred by deconvolution software for MS2 spectra within a run. The number of values in the tuple determines the quantile mode (minimum and maximum inclusive)." [PSI:MS]
is_a: MS:4000XXX ! mass accuracy metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! tuple
relationship: has_value_concept STATO:0000291 ! quantile
relationship: has_units UO:0000221 ! dalton
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: MS2 peak count quantiles
def: "Quantiles of the number of peaks detected per MS2 spectrum after peak picking. The number of values in the tuple determines the quantile mode (minimum and maximum inclusive)." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! tuple
relationship: has_value_concept STATO:0000291 ! quantile
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: MS2 peak count quantiles from deconvolution
def: "Quantiles of the number of fragment masses reported per MS2 spectrum after deconvolution. The number of values in the tuple determines the quantile mode (minimum and maximum inclusive)." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! tuple
relationship: has_value_concept STATO:0000291 ! quantile
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: amino acid gap count quantiles from deconvolution
def: "Quantiles of the number of putative amino acid gaps identified per deconvolved MSn spectrum, where each gap corresponds to a pair of fragment masses separated by the mass of an amino acid residue. The number of values in the tuple determines the quantile mode (minimum and maximum inclusive)." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! higher is better
relationship: has_value_type MS:4000XXX ! tuple
relationship: has_value_concept STATO:0000291 ! quantile
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: sequence tag length quantiles from deconvolution
def: "Quantiles of the lengths of the longest sequence tags inferred per deconvolved MSn spectrum. A sequence tag is defined as an unbroken series of fragment masses whose pairwise differences correspond to amino acid residue masses or equivalent tag inferences. The number of values in the tuple determines the quantile mode (minimum and maximum inclusive)." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! higher is better
relationship: has_value_type MS:4000XXX ! tuple
relationship: has_value_concept STATO:0000291 ! quantile
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: count of MS2 spectra with multiple amino acid gaps from deconvolution
def: "The number of MS2 spectra in a run whose deconvolved fragment mass lists contain at least three pairwise mass differences corresponding to amino acid residue masses." [PSI:MS]
comment: "Each amino acid gap represents a pair of fragment masses separated by the mass of an amino acid residue within a defined tolerance. Gaps are not required to form a continuous sequence. The metric counts how many MS2 spectra exhibit three or more such gaps, reflecting spectra that contain multiple residue-consistent mass differences and thus higher de novo interpretability."
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! higher is better
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: count of MS2 spectra with sequence tag length ≥ 3 from deconvolution
def: "The number of MS2 spectra in a run whose deconvolved fragment mass lists yield a contiguous sequence tag of at least three amino acids." [PSI:MS]
comment: "Each sequence tag represents an unbroken series of fragment masses whose pairwise differences correspond to amino acid residue masses. Only connected residue sequences are considered. The metric counts how many MS2 spectra produce a tag of length three or greater, reflecting the prevalence of spectra with extended sequence-informative fragmentation patterns."
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! run level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! higher is better
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: MSn spectrum reported in deconvolution output
def: "Boolean flag indicating whether an MSn spectrum reported in the peak file was also reported in the deconvolution output." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! spectrum level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! categorical
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000186 ! dimensionless unit
relationship: has_value_type xsd:boolean
[Term]
id: MS:4000XXX
name: precursor neutral mass from deconvolution
def: "Neutral precursor mass inferred by deconvolution for an individual MSn spectrum." [PSI:MS]
is_a: MS:4000XXX ! mass accuracy metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! spectrum level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000221 ! dalton
relationship: has_value_type xsd:float
[Term]
id: MS:4000XXX
name: fragment mass count from deconvolution
def: "The number of fragment masses reported for an individual MSn spectrum after deconvolution, where deconvolution combines signals from multiple isotopes and charge states corresponding to the same ion." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! spectrum level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: similarity degree of MSn spectrum
def: "The number of other MSn spectra judged similar to a given MSn spectrum based on overlapping fragment masses. This value corresponds to the node degree of the spectrum within the similarity graph constructed during clustering." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! spectrum level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: amino acid gap count from deconvolution
def: "The number of amino acid–consistent mass differences observed within the deconvolved fragment mass list for an individual MSn spectrum, where each gap corresponds to a pair of fragment masses separated by the mass of an amino acid residue." [PSI:MS]
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! data preprocessing stage
relationship: depends_on_data_type MS:4000XXX ! deconvoluted data
relationship: has_measurement_scope MS:4000XXX ! spectrum level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! context dependent
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int
[Term]
id: MS:4000XXX
name: length of longest sequence tag
def: "The amino acid length of the longest continuous sequence tag inferred from fragment mass differences corresponding to amino acid residue masses within an MSn spectrum. Longer tags indicate more complete fragmentation coverage and higher interpretability." [PSI:MS]
comment: "A sequence tag is formed by a continuous series of fragment masses whose pairwise differences correspond to amino acid residue masses. The longest tag length represents the maximum number of consecutive residue-consistent gaps within the spectrum."
is_a: MS:4000XXX ! spectral quality metric
relationship: part_of_workflow_stage MS:4000XXX ! identification stage
relationship: depends_on_data_type MS:4000XXX ! raw acquisition data
relationship: has_measurement_scope MS:4000XXX ! spectrum level
relationship: applies_to_acquisition_mode MS:4000XXX ! acquisition mode independent
relationship: has_quality_directionality MS:4000XXX ! higher is better
relationship: has_value_type MS:4000XXX ! single value
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:int