Handle Ambiguity of Protein Identifications from Shotgun Proteomics

Analyze ambiguous protein identifications using graph connected components (CCs)

The CCs4prot package allows to build a graph from shotgun proteomic identifications and calculate its connected components.

Reduce ambiguity of protein identifications by transcriptome-informed filtering

The CCs4prot package implements a transcriptome-informed filtering strategy to reduce ambiguity of protein identifications and allows to measure the impact of the filtering on ambiguity by assessment of the proportion and size of multi-protein CCs and by visual inspection of peptide-to-protein mappings for ambiguous identifications.

Install the CCs4prot R package

Download the package with the git clone command:

git clone https://github.com/laurafancello/CCs4prot.git

Initiate R and install the R package using devtools (devtools needs to be installed as well)

library("devtools")
devtools::install("CCs4prot")

Usage

To learn how to use CCs4prot, please refer to the introductory vignette posted at this link:

• [https://github.com/laurafancello/CCs4prot/blob/main/vignettes/IntroToCCs4prot.Rmd)

License

Distributed under the GPL-3 License.

Contact

Laura Fancello - laura.fancello@cea.fr
Thomas.Burger - thomas.burger@cea.fr