Run job on Sirius. — run • RuSirius

This function configures the job submission to Sirius. It creates an object of class config that can be used to submit a job Sirius, it can also be saved and reused later on through the saveJobConfig()function. For example on how to use, see the vignette.

Depending on what task you want to perform, you can specify the following parameters:

spectraMatchingParam: Allows to perform matching betweeen spectra input to spectral libraries.
formulaIdParam: Allows to generate molecular formula candidates for each features.
zodiacParam: Allows to perform re-ranking of formula candidates using Zodiac. It is advised to only perform it if De Novo structure annotation is run later.
predictParam: Allows to perform molecular fingeprint prediction using CSI:FingerID and compound classification using CANOPUS.
structureDbSearchParam: Allows to perform structure annotation based on the fingerprint identifications.
deNovoStructureParam: Allows to perform de novo structure generation using the MSNovelist tool.

Usage

run(
  sirius,
  compoundsIds = character(),
  alignedFeaturesIds = featuresId(sirius),
  fallbackAdducts = c("[M + H]+", "[M - H]-", "[M + Na]+", "[M + K]+"),
  enforceAdducts = character(),
  detectableAdducts = c("[M + H3N + H]+", "[M - H4O2 + H]+", "[M - H2O - H]-",
    "[M - H3N - H]-", "[M + Cl]-", "[2M + K]+", "[M + K]+", "[2M + Cl]-",
    "[M + C2H4O2 - H]-", "[M + H]+", "[2M + H]+", "[M - CH3 - H]-", "[M - H]-",
    "[M + Na]+", "[M - H2O + H]+"),
  spectraSearchParams = NA,
  formulaIdParams = NA,
  zodiacParams = NA,
  predictParams = NA,
  structureDbSearchParams = NA,
  msNovelistParams = NA,
  recompute = FALSE,
  configFile = character(),
  wait = TRUE
)

config(
  compoundsIds = character(),
  alignedFeaturesIds = character(),
  fallbackAdducts = c("[M + H]+", "[M - H]-", "[M + Na]+", "[M + K]+"),
  enforceAdducts = character(),
  detectableAdducts = c("[M + H3N + H]+", "[M - H4O2 + H]+", "[M - H2O - H]-",
    "[M - H3N - H]-", "[M + Cl]-", "[2M + K]+", "[M + K]+", "[2M + Cl]-",
    "[M + C2H4O2 - H]-", "[M + H]+", "[2M + H]+", "[M - CH3 - H]-", "[M - H]-",
    "[M + Na]+", "[M - H2O + H]+"),
  formulaIdParams = formulaIdParam(),
  zodiacParams = NA,
  predictParams = NA,
  structureDbSearchParams = NA,
  msNovelistParams = NA,
  spectraSearchParams = NA,
  recompute = FALSE
)

Arguments

sirius: Sirius object, the connection to the Sirius server.
compoundsIds: character vector, the ids of the compounds to process.
alignedFeaturesIds: character vector, the ids of the aligned features to process. By default, computes all.
fallbackAdducts: character vector, fallback adducts are considered if the auto detection did not find any indication for an ion mode.
enforceAdducts: character vector, the adducts to enforce. They are always considered.
detectableAdducts: character vector, detectable adducts are only considered if there is an indication in the MS1 scan (e.g. correct mass delta).
spectraSearchParams: object of class spectraMatchingParam, containing the parameters for the spectra matching.
formulaIdParams: object of class formulaIdParam, containing the parameters for the molecular formula identification.
zodiacParams: object of class zodiacParam, containing the parameters for the Zodiac re-ranking.
predictParams: object of class predictParam, containing the parameters for the molecular fingerprint prediction and compound classification.
structureDbSearchParams: object of class structureDbParam, containing the parameters for the structure annotation.
msNovelistParams: object of class deNovoStructureParam, containing the parameters for the de novo structure generation.
recompute: logical, whether to recompute the job , only necessary if the configfile comes from a saved file. Default is FALSE.
configFile: character, the path to the configuration file to use for the job submission, optional.
wait: logical, whether to wait for the job to finish. Default is TRUE

Value

The job ID of the submitted job, it can be inputted in the jobInfo() function to retrieve the job information. To retrieve results see results documentation.

Only formula identification

If you only want to perform formula identification, you can by only inputing the formulaIdParam object. In combination, you can also input the spectraMatchingParam object to perform spectral matching and subsequently compare the results.

Known molecular formula

If you already know the molecular formula for a compound, you can restrict SIRIUS to only consider that formula using the candidateFormulas parameter of formulaIdParam. This skips the de novo formula generation and instead computes the fragmentation tree for the specified formula(s) directly. Use the enforceAdducts parameter of run() to also fix the adduct type.

Structure annotation

To performe structure annotation, you need input the formulaIdParam object, as well as the predictParam object to perform molecular fingerprint prediction and compound classification. These results will then subsequently be used to perform structure annotation using the structureDbSearchParam object.

De Novo structure annotation

To perform de novo structure annotation, you need to input the formulaIdParam object, it is also advised in this case to perform re-ranking using the zodiacParam object. The molecular fingerprint prediction and compound classification can be performed using the predictParam object. The deNovoStructureParam object is then used to perform the de novo structure annotation.