The RiboMaP Spectral Annotation Method Applied to Various ADP-Ribosylome Studies Including INF-γ-Stimulated Human Cells and Mouse Tissues

• Published in: Frontiers in cardiovascular medicine Vol. 9; p. 851351
• Main Authors: Singh, Sasha A, Kuraoka, Shiori, Pestana, Diego Vinicius Santinelli, Nasir, Waqas, Delanghe, Bernard, Aikawa, Masanori
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 28-03-2022
• Subjects: Cardiovascular Medicine; mass spectrometry; PARP14; post-translational modification; ribosylation; SEQUEST; SEQUEST; mass spectrometry; post-translational modification; PARP14; ribosylation
• ISSN: 2297-055X; 2297-055X
• DOI: 10.3389/fcvm.2022.851351

ADP-ribosylation is a post-translational modification that is catalyzed by the ADP-ribosyltransferase enzyme family. Major emphasis to date has been ADP-ribosylation's role in cancer; however, there is growing interest in its role in inflammation and cardiovascular disease. Despite a recent boom in ADP-ribosylation mass spectrometry-based proteomics, there are limited computational resources to evaluate the quality of reported ADP-ribosylated (ADPr) proteins. We recently developed a novel mass spectral annotation strategy (RiboMaP) that facilitates identification and reporting of ADPr peptides and proteins. This strategy can monitor the fragmentation properties of ADPr peptide-unique fragment ions, termed m-ions and p-ions, that in turn provide spectral quality scores for candidate ADP-ribosyl peptides. In this study, we leveraged the availability of publicly available ADP-ribosylome data, acquired on various mass spectrometers, to evaluate the broader applicability of RiboMaP. We observed that fragmentation spectra of ADPr peptides vary considerably across datasets; nonetheless, RiboMaP improves ADPr peptide spectral annotation across all studies. We then reanalyzed our own previously published
ADP-ribosylome data to determine common responses to the pro-inflammatory cytokine, IFN-γ. We conclude that despite these recent advances in the field of ADPr proteomics, studies in the context of inflammation and cardiovascular disease still require further bench-to-informatics workflow development in order to capture ADPr signaling events related to inflammatory pathways.