Find features using SIRIUS

Uses SIRIUS to find features.

Usage

findFeaturesSIRIUS(
  analysisInfo,
  noiseIntensity = NULL,
  alignMaxRTDev = NULL,
  minSNR = NULL,
  login = "check",
  alwaysLogin = FALSE,
  projectPath = NULL,
  runMode = "execute",
  SIRIUSAPI = NULL,
  verbose = TRUE
)

importFeaturesSIRIUS(input, analysisInfo, ...)

Arguments

analysisInfo

A data.frame (or data.table) with Analysis information.

noiseIntensity, alignMaxRTDev, minSNR

Parameters for the SIRIUS feature finding algorithm. See the SIRIUS documentation for details. Set to NULL to use the default values.

login, alwaysLogin

Specifies if and how account logging of SIRIUS should be handled:

login=FALSE: no automatic login is performed and the active login status is not checked.

login="check": aborts if no active login is present.

login="interactive": interactively ask for login (using getPass).

login=c(username="...", password="..."): perform the login with the given details. For security reasons, please do not enter the details directly, but use e.g. environment variables or store/retrieve them with the keyring package.

if alwaysLogin=TRUE then a login is always performed, otherwise only if SIRIUS reports no active login.

See the SIRIUS website and patRoon handbook for more information.

NOTE: By loggin in you will accept the terms of the Service and Privacy Policy of the SIRIUS Webservice.

runMode, projectPath

Whether to execute a SIRIUS processing job (runMode="execute") or load results from an existing SIRIUS project (runMode"read"). If runMode="execute" then projectPath can be NULL and a temporary project will be used, otherwise projectPath must point to an existing project.

NOTE: if runMode="execute" then any existing project at projectPath will be removed.

NOTE: This is primarily intended for internal purposes, but may be of interest to e.g. re-import SIRIUS results.

(sets workflow) projectPath should be a character specifying the paths for each set.

SIRIUSAPI

An rsirius_api object for connecting to the SIRIUS API. If NULL, a new connection will be started automatically.

verbose

If set to FALSE then no text output is shown.

input

Sets projectPath.

...

Additional arguments passed to findFeaturesSIRIUS.

Value

An object of a class which is derived from features.

Details

This function uses SIRIUS to automatically find features. This function is called when calling findFeatures with algorithm="sirius".

The MS files should be in the mzML or mzXML format.

The input MS data files need to be centroided. The convertMSFiles function can be used to centroid data.

importFeaturesSIRIUS is a simple wrapper around findFeaturesSIRIUS to import features from an existing SIRIUS project. It will set runMode="read" and projectPath to the provided input path.

Running SIRIUS

By default, patRoon tries to connect to a running instance of SIRIUS. This is generally faster and may be useful for debugging by e.g. checking the logs in SIRIUS. Otherwise, an attempt will be made to start SIRIUS automatically. The binaries are searched from the patRoon.path.SIRIUS package option, patRoonExt package or the system PATH environment variable. Any automatically started SIRIUS instances are automatically closed if jobs are finished. By default, a temporary SIRIUS project is made for SIRIUS data processing and removed afterwards. See the projectPath to change this.

SIRIUS 6 functionality

The interface to SIRIUS 6 is still in development and may be extended in the future. There is a vast amount of functionality available, which will require quite some effort to support all. However, the current functionality in patRoon is mostly equal to what was supported with previous SIRIUS releases. Any feedback on the inclusion of specific functionality is welcome!

References

Hoffmann MA, Nothias L, Ludwig M, Fleischauer M, Gentry EC, Witting M, Dorrestein PC, Dührkop K, Böcker S (2021). “High-confidence structural annotation of metabolites absent from spectral libraries.” Nature Biotechnology, 40(3), 411–421. ISSN 1546-1696. doi:10.1038/s41587-021-01045-9 . http://dx.doi.org/10.1038/s41587-021-01045-9.

Dührkop K, Nothias L, Fleischauer M, Reher R, Ludwig M, Hoffmann MA, Petras D, Gerwick WH, Rousu J, Dorrestein PC, Böcker S (2020). “Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.” Nature Biotechnology, 39(4), 462–471. ISSN 1546-1696. doi:10.1038/s41587-020-0740-8 . http://dx.doi.org/10.1038/s41587-020-0740-8.

Duhrkop K, Fleischauer M, Ludwig M, Aksenov AA, Melnik AV, Meusel M, Dorrestein PC, Rousu J, Bocker S (2019). “SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information.” Nature Methods, 16(4), 299–302. doi:10.1038/s41592-019-0344-8 .

Duhrkop K, Bocker S (2015). “Fragmentation Trees Reloaded.” In Przytycka TM (ed.), Research in Computational Molecular Biology, 65–79. ISBN 978-3-319-16706-0.

Duhrkop K, Shen H, Meusel M, Rousu J, Bocker S (2015). “Searching molecular structure databases with tandem mass spectra using CSI:FingerID.” Proceedings of the National Academy of Sciences, 112(41), 12580–12585. doi:10.1073/pnas.1509788112 .

Bocker S, Letzel MC, Liptak Z, Pervukhin A (2008). “SIRIUS: decomposing isotope patterns for metabolite identification.” Bioinformatics, 25(2), 218–224. doi:10.1093/bioinformatics/btn603 .