An R script implemented as a demo for processing multiple LC-MS/MS files accompanying the manuscript: "IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data". The source code of the IsoForma package and documentation in vignettes are available at https://github.com/EMSL-Computing/isoforma-lib.
- Download and install R: https://ftp.osuosl.org/pub/cran/
- Download, install, and open RStudio (Free version): https://www.rstudio.com/products/rstudio/download/
- If re-installing, remove any previous versions of pspecter remove.packages("pspecterlib")
- Clone/download IsoForma-paper repository
- Open IsoForma_demo.R in RStudio
- Install packages executing lines 6-10
- Update the path in line 19 according to the location of the data in your computer
- Execute all code in the script. Press Ctrl+Alt to select all code and Ctrl+Enter to execute it.
- Parameters.xlsx
- Targets.xlsx
- RawData folder contains 2 mzML files converted using MSConvert (v. 3.0.22139-aa8be89) using parameters: scan time 5400-7800 seconds, vendor peak picking and ms levels 1-2.
If you use IsoForma or any portions of this code please cite: Degnan et al. "IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data". Submitted to Journal of Proteome Research.