crisscrosslinkeR: identification and visualization of protein-RNA and protein-protein interactions from crosslinking mass spectrometry

Emma H Gail; Anup D Shah; Ralf B Schittenhelm; Chen Davidovich

doi:10.1093/bioinformatics/btaa1043

crisscrosslinkeR: identification and visualization of protein-RNA and protein-protein interactions from crosslinking mass spectrometry

Bioinformatics. 2021 Apr 1;36(22-23):5530-5532. doi: 10.1093/bioinformatics/btaa1043.

Authors

Emma H Gail^{1

2}, Anup D Shah^{1

2

3

4}, Ralf B Schittenhelm^{1

2

3}, Chen Davidovich^{1

2

5}

Affiliations

¹ Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Victoria 3800, Australia.
² Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia.
³ Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
⁴ Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
⁵ EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, Victoria 3800, Australia.

PMID: 33346827
DOI: 10.1093/bioinformatics/btaa1043

Abstract

Summary: Unbiased detection of protein-protein and protein-RNA interactions within ribonucleoprotein complexes are enabled through crosslinking followed by mass spectrometry. Yet, different methods detect different types of molecular interactions and therefore require the usage of different software packages with limited compatibility. We present crisscrosslinkeR, an R package that maps both protein-protein and protein-RNA interactions detected by different types of approaches for crosslinking with mass spectrometry. crisscrosslinkeR produces output files that are compatible with visualization using popular software packages for the generation of publication-quality figures.

Availability and implementation: crisscrosslinkeR is a free and open-source package, available through GitHub: github.com/egmg726/crisscrosslinker.

Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract

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