{fioRa} 0.2.5

FIORA is an in silico fragmentation algorithm designed to predict tandem mass spectra (MS/MS) with high accuracy. Using a graph neural network, FIORA models bond cleavages, fragment intensities, and estimates retention times (RT) and collision cross sections (CCS).

The original model and prediction algorithm is implemented in Python and can be found at its GitHub Repo. The full description of the algorithm is published in a Nature Communications article.

The R package {fioRa} provides a wrapper for FIORA, to either run the Python script using the R function run_script() or start a GUI (Shiny-App) using the R function run_app().

Installation

You can install the development version of {fioRa} from GitHub.

install.packages("devtools")
devtools::install_github("janlisec/fioRa")

Before first use you need to set up a python installation and a virtual environment fiora which can be achieved from within R with the help of the reticulate package.

# [1] install R package reticulate if you haven't done yet
install.packages("reticulate")

# [2] install python (miniconda) if you haven't done yet
if (!file.exists(reticulate::miniconda_path())) {
  reticulate::install_miniconda(path = reticulate::miniconda_path(), update = FALSE, force = FALSE)
}

# [3] install python module fiora in a virtual environment
if (!reticulate::virtualenv_exists("fiora")) {
  reticulate::virtualenv_create("fiora")
  reticulate::virtualenv_install(envname = "fiora", packages = "git+https://github.com/BAMeScience/fiora.git")
}

Run

Now, you can launch the application as a Shiny-App.

fioRa::run_app()

fioRa screenshot

Alternatively you can use the exported function run_script() to work in the R command line directly. This will accept R styled input parameters, generate an appropriate temporary FIORA input file, process it and return an R styled list including the predicted MS/MS spectrum.

fioRa::run_script(Name = "Example_0", SMILES = "CC1=CC(=O)OC2=CC(OS(O)(=O)=O)=CC=C12")
#> No valid default_path provided, using reticulate::miniconda_path.
#> $Example_0
#> $Example_0$TITLE
#> [1] "Example_0"
#> 
#> $Example_0$SMILES
#> [1] "CC1=CC(=O)OC2=CC(OS(O)(=O)=O)=CC=C12"
#> 
#> $Example_0$FORMULA
#> [1] "C10H8O6S"
#> 
#> $Example_0$PRECURSOR_MZ
#> [1] "254.99688252391005"
#> 
#> $Example_0$PRECURSORTYPE
#> [1] "[M-H]-"
#> 
#> $Example_0$COLLISIONENERGY
#> [1] "17.0"
#> 
#> $Example_0$INSTRUMENTTYPE
#> [1] "HCD"
#> 
#> $Example_0$COMMENT
#> [1] "\"In silico generated spectrum by Fiora OS v0.1.0\""
#> 
#> $Example_0$spec
#>           mz         int
#> 1   78.94844 0.001667393
#> 2   79.95681 0.022089725
#> 3   80.96409 0.028634388
#> 4   81.97246 0.002399962
#> 5  159.04406 0.002223121
#> 6  173.02332 0.002690818
#> 7  174.03169 0.004479981
#> 8  175.03897 0.394105196
#> 9  176.04734 0.003682357
#> 10 177.05462 0.025992798
#> 11 239.97286 0.004418257
#> 12 254.99688 0.494040728

About

You are reading the doc about version 0.2.5 compiled on 2025-06-25 09:43:37.961743.