Engine dedicated to Mass Spectrometry (MS) data processing
Source:R/class_Engine_MassSpecEngine.R
MassSpecEngine.RdThe MassSpecEngine R6 class is a framework for parsing, processing and inspecting mass spectrometry (MS) data. The engine has MassSpec as data type. The Analyses active field has class MassSpecAnalyses, where MS data (i.e., spectra and chromatograms, including chromatograms produced by UV detection) can be loaded from mzML and mzXML. See methods MassSpecAnalyses for more details. If msconvert from ProteoWizard is installed and found via CLI (i.e., must be added to the environmental variables), the engine can also load vendor formats (i.e., Agilent MassHunter .d, Thermo Scientific RAW, Shimadzu LCD (except ITOF), Sciex WIFF /WIFF2) by direct conversion to mzML. Note that conversion of vendor formats is only possible under Windows OS. The results active field is a list that can hold the classes: MassSpecResults_NonTargetAnalysis, MassSpecSpectra and Chromatograms. Note that the MassSpecEngine is a subclass of Engine and inherits all methods from the parent class.
Note
The MassSpecEngine is using several patRoon assets for assembly of Non-Target Analysis (NTA) data processing workflows.
References
Helmus R, ter Laak TL, van Wezel AP, de Voogt P, Schymanski EL (2021). “patRoon: open source software platform for environmental mass spectrometry based non-target screening.” Journal of Cheminformatics, 13(1). doi:10.1186/s13321-020-00477-w .
Helmus R, van de Velde B, Brunner AM, ter Laak TL, van Wezel AP, Schymanski EL (2022). “patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening.” Journal of Open Source Software, 7(71), 4029. doi:10.21105/joss.04029 .
Kapoulkine A (2022). “pugixml 1.13: Light-weight, simple and fast XML parser for C++ with XPath support.” Copyright (C) 2006-2018. http://pugixml.org.
Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008). “ProteoWizard: open source software for rapid proteomics tools development.” Bioinformatics, 24(21), 2534–2536. doi:10.1093/bioinformatics/btn323 , http://www.ncbi.nlm.nih.gov/pubmed/18606607.
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak M, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P (2012). “A cross-platform toolkit for mass spectrometry and proteomics.” Nature Biotechnology, 30(10), 918–920. https://doi.org/10.1038/nbt.2377.
Super class
StreamFind::Engine -> MassSpecEngine
Active bindings
MassSpecResults_NonTargetAnalysisGet/Set for the
MassSpecResults_NonTargetAnalysisresults class.MassSpecResults_SpectraGet/set for the
MassSpecResults_Spectraresults class.MassSpecResults_ChromatogramsGet/set for the MassSpecResults_Chromatograms results class.
Methods
Inherited methods
StreamFind::Engine$clear_cache()StreamFind::Engine$clear_results()StreamFind::Engine$get_cache_info()StreamFind::Engine$get_cache_size()StreamFind::Engine$has_analyses()StreamFind::Engine$has_results()StreamFind::Engine$load()StreamFind::Engine$print()StreamFind::Engine$run()StreamFind::Engine$run_app()StreamFind::Engine$run_workflow()StreamFind::Engine$save()
Method new()
Creates an R6 MassSpecEngine class object.
Usage
MassSpecEngine$new(
metadata = NULL,
workflow = NULL,
analyses = NULL,
centroid = FALSE,
levels = c(1, 2)
)Arguments
metadataA named list or a
Metadataobject. Each list element must have length one. There is no type restrictions except for name (must be type character), author (must be type character) and date (must be class POSIXct or POSIXt). A file entry must be a character string with a full path to a file.workflowA
Workflowobject, a list ofProcessingStepobjects or a character string with a full path to a rds or json file containing aWorkflow.analysesA MassSpecAnalyses class object or a
character vectorwith full file paths to mzML files or adata.framewithcolnames: "file", "replicate" and "blank". The "replicate" column is used to group the analyses and the "blank" column is used to identify the blank samples. The "file" column is the full path to the mzML files. Ifmsconvertfrom ProteoWizard is installed and found via CLI (i.e., must be added to the environmental variables), the engine can also load vendor formats (i.e., Agilent MassHunter .d, Thermo Scientific RAW, Shimadzu LCD (except ITOF), Sciex WIFF / WIFF2) by direct conversion to mzML. Note that conversion of vendor formats is only possible under Windows OS.centroidLogical (length 1). Set to
TRUEto centroid data when converting from vendor formats to mzML.levelsNumeric vector with the MS levels to consider when centroiding data. Default is
c(1, 2).
Method add_analyses()
Adds analyses. Note that when adding new analyses, any existing results are removed.
Arguments
analysesA character vector with full file paths to mzML/mzXML files. f
msconvertfrom ProteoWizard is installed and found via CLI (i.e., must be added to the environmental variables), the engine can also load vendor formats (i.e., Agilent MassHunter .d, Thermo Scientific RAW, Shimadzu LCD (except ITOF), Sciex WIFF/WIFF2) by direct conversion to mzML. Note that conversion of vendor formats is only possible under Windows OS.
Method set_replicate_names()
Set replicate names to the analysis, using a character vector with the same length as the number of analyses.
Method set_blank_names()
Set blank names to the analysis, using a character vector with the same length as the number of analyses. Note that the names must be one of the replicate names.