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The RiboMaP Spectral Annotation Method Applied to Various ADP-Ribosylome Studies Including INF-γ-Stimulated Human
Sasha A Singh1, Shiori Kuraoka1, Diego Vinicius Santinelli Pestana1
1Department of Medicine, Center for Interdisciplinary Cardiovascular Sciences, Brigham Women's Hospital and Harvard Medical School, Boston, MA, United States.
Abstract:
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 in vitro 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.
Insights
ADP-ribosylation (ADPr) is crucial in disease. A new tool, RiboMaP, improves the analysis of ADPr proteins from mass spectrometry data, aiding research in inflammation and cardiovascular disease.
Area of Science:
- Biochemistry
- Proteomics
- Bioinformatics
Background:
- ADP-ribosylation is a key post-translational modification with roles in cancer, inflammation, and cardiovascular disease.
- Despite advances in ADP-ribosylation mass spectrometry, computational tools for assessing data quality are limited.
- Accurate identification of ADP-ribosylated proteins is essential for understanding cellular signaling.
Purpose of the Study:
- To evaluate the broad applicability of the RiboMaP annotation strategy for ADP-ribosylated peptides across diverse mass spectrometry datasets.
- To assess the effectiveness of RiboMaP in improving spectral annotation quality for ADP-ribosylated proteins.
- To investigate ADP-ribosylation responses to IFN-γ in the context of inflammation.
Main Methods:
- Leveraged publicly available ADP-ribosylome datasets from various mass spectrometers.
- Applied the RiboMaP strategy to analyze fragmentation spectra of ADP-ribosylated peptides, focusing on m-ions and p-ions.
- Reanalyzed in vitro ADP-ribosylome data to identify responses to IFN-γ.
Main Results:
- RiboMaP demonstrated improved spectral annotation of ADP-ribosylated peptides across different datasets, despite variations in fragmentation spectra.
- The study confirmed the utility of RiboMaP in enhancing the reliability of ADP-ribosylation identification.
- Analysis revealed insights into ADP-ribosylation signaling pathways related to inflammation.
Conclusions:
- RiboMaP is a valuable computational resource for improving the quality assessment of ADP-ribosylated proteins identified by mass spectrometry.
- Further development of bioinformatics workflows is needed for comprehensive analysis of ADP-ribosylation in inflammation and cardiovascular disease research.
- Enhanced data analysis tools are critical for fully elucidating the role of ADP-ribosylation in diverse biological processes.
