ScaffoldMS R package

Enhanced analysis of protein mass spectrometry results provided by Scaffold Proteome software ©.

Installation

## using install_gitlab
remotes::install_gitlab(
    "aurelien.brionne/ScaffoldMS",
    host = "forgemia.inra.fr",
    build_opts = c("--no-resave-data", "--no-manual")
)

## alternative (from local directory)
    # clone package (from prompt)
    git clone https://forgemia.inra.fr/aurelien.brionne/ScaffoldMS.git

    # build package (from R console) 
    devtools::build("ScaffoldMS")

    # install package (from R console)
    install.packages("ScaffoldMS_1.2.1.tar.gz", repos = NULL, type = "source")

Quick overview

1. Annotate proteins: ScaffoldMS::annotate.

• Identification of the species of origin from Genbank data (taxon, scientific name, common name).
• Gene annotation summary.
• construction of the peptide signature ("pattern") allowing the identification of proteins and their grouping using Blast + suite and clustal omega.

2. perform Linear model statistics from Scaffold Proteome software © quantification files (current view): ScaffoldMS::quantify.

3. Merge pattern alignments (clustalo and blast) results: ScaffoldMS::merge_alignments.

4. Display proteins species count overview: ScaffoldMS::species_count.

5. Proteins abundance profiling: ScaffoldMS::HCL.

6. Proteins abundance plot: ScaffoldMS::abundance_plot.