PeptideShaker

PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines

http://compomics.github.io/projects/peptide-shaker.html

SearchGUI

SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines and de novo sequencing algorithms.

http://compomics.github.io/projects/searchgui.html

Academic literature review

• Mehta, Subina; Bernt, Matthias; Chambers, Matthew et al. (2023). A Galaxy of informatics resources for MS-based proteomics. (external link)

Academic article

• Farag, Yehia Mokhtar; Horro Marcos, Carlos; Vaudel, Marc et al. (2021). PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data. (external link)
• Hernández Sánchez, Luis Francisco; Burger, Bram; Horro Marcos, Carlos et al. (2019). PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping. (external link)

See a complete overview of publications in Cristin.

Contributing to PeptideShaker (http://compomics.github.io/projects/peptide-shaker.html), SearchGUI (http://compomics.github.io/projects/searchgui.html) and their integration into Galaxy (https://galaxyproject.org/).