metstats

Library for standardized analysis and visualization of metabolomics data

Calico Life Sciences, LLC

Demo analysis of Metabolomics Workbench ST003519 published in quarto pub

Analysis workflow

1. Convert mass spec raw files to mzML using ProteWizard MSConvert software. e.g. Metabolomics Workbench ST003519 for demo, raw files are already mzML.

2. Generate an mzrollDB file for the mzML files using the MAVEN GUI, or in R using the peakdetector executable and R pipeline support. See guidelines here

3. Open mzrollDB in MAVEN 2 software and annotate peaks.

4. Create a project folder and put the following files in the folder:

• Annotated mzrollDB file
• qmd file metstats/vignettes/ST003519_demo.Qmd for the demo

5. In terminal go to the project folder and run the following to set up a new Quarto website project:

quarto create project my-website

• Choose a folder name for the project/website.

6. Render the qmd to generate html webpage in localhost.

7. To publish html to Quarto pub, run the following in terminal:

quarto publish quarto-pub ST003519_demo.qmd

• a Quarto pub account is required for publishing.

Network Analysis

To run Cytoscape and generate metabolic networks:

1. Download latest version of Cytoscape

2. Install RCy3 2.5.1 Cytoscape-R API

• Newer versions of RCy3 are problematic.
• Recommended method of installation:

# Clone the RCy3 repository via terminal:
git clone git@github.com:delfarahalireza/RCy3.git

# Install the package from source in R:
install.packages("cloned directory of RCy3", repos = NULL, type = "source")

# Restart R session and load RCy3
library(RCy3)

# Check that version of RCy3 is 2.5.1 after loading library(Rcy3)
packageVersion("RCy3")

3. Open metstats/inst/extdata/Networks.cys file

4. In R, run the network plots, pathways color, pathways shape, and pathways chunks similar to metstats/vignettes/ST003519_demo.Qmd