DEP

DEP (Differential Enrichment analysis of Proteomics data) is an open-source R software package designed to analyze data generated from the ubiquitin interactor affinity enrichment-mass spectrometry (UbIA-MS) method. UbIA-MS is used to identify proteins interacting with different types of ubiquitin chains in cell lysates. DEP provides a user-friendly graphical interface and computational tools to process and analyze the mass spectrometry data obtained from UbIA-MS experiments. The software identifies proteins that are differentially enriched between samples, helping researchers understand the role of ubiquitin-binding proteins in various cellular processes and how they respond to different stimuli or cell types.

Topic

Proteomics experiment;Proteomics

Detail

  • Operation: Differential gene expression analysis

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.26.0

  • Credit: The “Hundred Talents Program C” of the Chinese Academy of Sciences, Guangdong Science and Technology Projects, the NWO Gravitation program, the ERC grant Ubicode, the EMBL Interdisciplinary Postdoc (EIPOD) Programme under a grant from the Marie Sklodowska-Curie Actions COFUND.

  • Input: -

  • Output: -

  • Contact: Arne Smits smits.arne@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Proteome-wide identification of ubiquitin interactions using UbIA-MS.
  • Zhang X, Smits AH, van Tilburg GB, Ovaa H, Huber W, Vermeulen M. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nat Protoc. 2018 Mar;13(3):530-550. doi: 10.1038/nprot.2017.147. Epub 2018 Feb 15. PMID: 29446774.
  • https://doi.org/10.1038/nprot.2017.147
  • PMID: 29446774
  • PMC: -

Download and documentation

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