Getting Started with RuSirius

library(RuSirius)
#> Warning: package 'generics' was built under R version 4.6.1

Introduction

Note: this vignette is pre-computed. See the session info for information on packages used and the date the vignette was rendered. The vignette requires a running Sirius instance. To reproduce this analysis, you will need Sirius 6.5 installed and running.

RuSirius provides an R interface to the Sirius mass spectrometry software for metabolite identification. This vignette covers the basics of connecting to Sirius and managing projects.

Prerequisites

Before using RuSirius, you need:

Sirius 6.5 installed on your system. Download from the official releases page.
A Sirius account (free registration at bright-giant.com)

Connecting to Sirius

The Sirius() function creates a connection to the Sirius application. If Sirius is not running, it will attempt to start it automatically. The port parameter allows to configure the Sirius application to use a particular port; this is required when using the Docker container (where Sirius is pre-started on port 9999), but generally the function can be used without specifying a port.

# Basic connection - Sirius will start if not running
srs <- Sirius(port = 9999)
srs
#> Sirius object
#> Valid connection to Sirius:  TRUE 
#> Logged In:  TRUE 
#> Sirius version:  6.5.4 
#> Sirius update available:  FALSE 
#> No project is currently loaded

If you have credentials, you can log in during connection:

srs <- Sirius(
    username = "[email protected]",
    password = "your_password",
    port = 9999
)

Checking Connection Status

You can verify your connection is valid with checkConnection(srs):

# Check if connected
checkConnection(srs)
#> [1] TRUE

# View connection details
srs
#> Sirius object
#> Valid connection to Sirius:  TRUE 
#> Logged In:  TRUE 
#> Sirius version:  6.5.4 
#> Sirius update available:  FALSE 
#> No project is currently loaded

Managing Projects

Sirius organizes data and results into projects. You can create new projects or open existing ones during connection, or later using the openProject() function. Parameters projectId and path allow to set the name (ID) of the project and the path to the directory where the project file should be stored in.

Creating/Opening a Project

# Open a project on the existing connection
srs <- openProject(srs, projectId = "my_analysis", path = getwd())

The project file will be saved as my_analysis.sirius in the specified path.

Project Information

# Get project details
projectInfo(srs)
#> $projectId
#> [1] "my_analysis"
#> 
#> $location
#> [1] "C:\\Users\\phili\\AppData\\Local\\Temp\\claude\\E--GitHub-RuSirius\\1afa4ba5-deea-4f05-82c3-5cfe3d2bdc91\\scratchpad\\vig_run\\my_analysis.sirius"
#> 
#> $type
#> [1] "UNIMPORTED"
#> 
#> $compatible
#> [1] TRUE
#> 
#> $numOfFeatures
#> [1] 0
#> 
#> $numOfCompounds
#> [1] 0
#> 
#> $numOfBytes
#> [1] 8192

# List all open projects
listOpenProjects(srs)
#> [1] "my_analysis"

Working with Features

After importing data (see the “Importing Spectra” vignette), you can manage features:

# List feature IDs
featuresId(srs)
#> character(0)

# Get feature information
featuresInfo(srs)
#> NULL

# Get the mapping between your IDs and Sirius IDs
srs@featureMap
#> data frame with 0 columns and 0 rows

Logging In

If you didn’t provide credentials at connection time:

srs <- logIn(srs, username = "[email protected]",
             password = "your_password")

Using the GUI

You can open the Sirius graphical interface for visual exploration:

# Open the GUI
openGUI(srs)

# Close the GUI when done
closeGUI(srs)

Shutting Down

Always properly close your connection when finished:

# Close project and shutdown
shutdown(srs, closeProject = TRUE)
#> There does not seem to be any process or process_id to shut down...

Utility Functions

RuSirius provides several utility functions. See ?utils for the full list:

checkConnection() - Verify connection status
logIn() - Log in to Sirius
openProject() / listOpenProjects() - Project management
projectInfo() - Get project details
featuresId() / featuresInfo() - Feature management
deleteFeatures() - Remove features
mapFeatures() - Get ID mappings
openGUI() / closeGUI() - GUI control
shutdown() - Clean shutdown

Next Steps

See the “Importing Spectra into Sirius” vignette for importing MS data
See ?run for running Sirius computations (formula ID, structure search, etc.)
See ?results for retrieving annotation results

Session Info

sessionInfo()
#> R version 4.6.0 (2026-04-24 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 26300)
#> 
#> Matrix products: default
#>   LAPACK version 3.12.1
#> 
#> locale:
#> [1] LC_COLLATE=English_United Kingdom.utf8 
#> [2] LC_CTYPE=English_United Kingdom.utf8   
#> [3] LC_MONETARY=English_United Kingdom.utf8
#> [4] LC_NUMERIC=C                           
#> [5] LC_TIME=English_United Kingdom.utf8    
#> 
#> time zone: Europe/Paris
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#> [1] RuSirius_1.0.6      Spectra_1.22.2      BiocParallel_1.46.0
#> [4] S4Vectors_0.50.1    BiocGenerics_0.58.1 generics_0.1.4     
#> [7] RSirius_6.5.4       ProtGenerics_1.44.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] tidyselect_1.2.1            dplyr_1.2.1                
#>  [3] farver_2.1.2                blob_1.3.0                 
#>  [5] Biostrings_2.80.1           filelock_1.0.3             
#>  [7] S7_0.2.2                    bitops_1.0-9               
#>  [9] fastmap_1.2.0               lazyeval_0.2.3             
#> [11] RCurl_1.98-1.19             BiocFileCache_3.2.0        
#> [13] digest_0.6.39               lifecycle_1.0.5            
#> [15] cluster_2.1.8.2             rsvg_2.7.0                 
#> [17] KEGGREST_1.52.2             RSQLite_3.53.3             
#> [19] magrittr_2.0.5              compiler_4.6.0             
#> [21] rlang_1.2.0                 tools_4.6.0                
#> [23] yaml_2.3.12                 igraph_2.3.3               
#> [25] data.table_1.18.4           knitr_1.51                 
#> [27] S4Arrays_1.12.0             htmlwidgets_1.6.4          
#> [29] curl_7.1.0                  bit_4.6.0                  
#> [31] DelayedArray_0.38.2         plyr_1.8.9                 
#> [33] xml2_1.6.0                  RColorBrewer_1.1-3         
#> [35] abind_1.4-8                 purrr_1.2.2                
#> [37] grid_4.6.0                  ggplot2_4.0.3              
#> [39] scales_1.4.0                MASS_7.3-65                
#> [41] MultiAssayExperiment_1.38.0 SummarizedExperiment_1.42.0
#> [43] cli_3.6.6                   crayon_1.5.3               
#> [45] otel_0.2.0                  httr_1.4.8                 
#> [47] reshape2_1.4.5              rjson_0.2.23               
#> [49] DBI_1.3.0                   cachem_1.1.0               
#> [51] stringr_1.6.0               parallel_4.6.0             
#> [53] AnnotationDbi_1.74.0        BiocManager_1.30.27        
#> [55] XVector_0.52.0              AnnotationFilter_1.36.0    
#> [57] matrixStats_1.5.0           base64enc_0.1-6            
#> [59] vctrs_0.7.3                 Matrix_1.7-5               
#> [61] jsonlite_2.0.0              IRanges_2.46.0             
#> [63] bit64_4.8.2                 clue_0.3-68                
#> [65] tidyr_1.3.2                 glue_1.8.1                 
#> [67] codetools_0.2-20            QFeatures_1.22.0           
#> [69] DT_0.34.0                   stringi_1.8.7              
#> [71] gtable_0.3.6                BiocVersion_3.23.1         
#> [73] GenomicRanges_1.64.0        tibble_3.3.1               
#> [75] MetaboAnnotation_1.16.0     pillar_1.11.1              
#> [77] rappdirs_0.3.4              htmltools_0.5.9            
#> [79] Seqinfo_1.2.0               R6_2.6.1                   
#> [81] dbplyr_2.6.0                httr2_1.2.3                
#> [83] evaluate_1.0.5              Biobase_2.72.0             
#> [85] lattice_0.22-9              AnnotationHub_4.2.1        
#> [87] png_0.1-9                   memoise_2.0.1              
#> [89] MetaboCoreUtils_1.20.1      Rcpp_1.1.1-1.1             
#> [91] SparseArray_1.12.2          gridExtra_2.3.1            
#> [93] CompoundDb_1.16.0           ChemmineR_3.64.0           
#> [95] xfun_0.59                   MsCoreUtils_1.24.0         
#> [97] fs_2.1.0                    MatrixGenerics_1.24.0      
#> [99] pkgconfig_2.0.3