/isoforma-lib

R package for the relative quantitation of proteoforms with MS2 fragmentation patterns

Primary LanguageRBSD 2-Clause "Simplified" LicenseBSD-2-Clause

isoforma-lib

R package for the relative quantification of proteoform positional isomers (QPI) from MS2 scan data

IsoForma_Logo

How to install

devtools::install_github("EMSL-Computing/isoforma-lib")

To get started, read our vignette

You may need to install pspecterlib separately, though it should auto-install with the above command. If not, try the command below. Check that both packages install with library(isoforma) and library(pspecterlib). If one of the packages does not install,

devtools::install_github("EMSL-Computing/pspecterlib")

Installation Checks

The package has been succesfully installed on an Apple M1 Max using 13.6.1 and a Windows PC running Windows 11. We encourage users to please report any installation issues on the Github Issues page, and we are more than happy to help!

Usage (Windows)

  1. Download and install R: https://ftp.osuosl.org/pub/cran/
  2. Download, install, and open RStudio (Free version): https://www.rstudio.com/products/rstudio/download/
  3. If re-installing, remove any previous versions of pspecter remove.packages("pspecterlib")
  4. Clone/download IsoForma-paper repository

Reference

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.

Modifications

For a list of acceptable modifications, see the "Modification" column of Glossary. If there is a modification needed that is not in this list, please report the modification to our issues page.