Mass spectrometry-based proteomics has become a near-ubiquitous tool in the routine characterization of proteoforms. Both 'bottom-up' methods, which involve enzymatic digestion of proteins of interest prior to chromatographic separation and mass analysis, and 'top-down' methods, which instead analyze intact proteins without digestion, have expanded the understanding of the dynamic distribution of proteins and their post-translational modification landscape within cells. Moreover, advances in high-resolution mass spectrometers, tandem mass spectrometry (MS/MS) modes, and post-processing methods have all contributed to the extension of top-down analysis to progressively larger proteins and protein complexes. The original top-down studies of proteins typically used conventional collisional activation dissociation (CAD) for MS/MS. CAD effectively fragmented peptides and small proteins (<10 kDa) by generation of predominantly b/y fragments. However, its substantial dependence on precursor charge and preference for specific cleavages based on primary sequence has limited its utility for large proteins (>30 kDa). In addition, the stepwise vibrational excitation process via multiple collisions favors cleavage of the most labile bonds, potentially resulting in loss of PTMs and impeding their localization. To achieve more comprehensive fragmentation throughout the protein backbone, several higher-energy dissociation techniques have been developed for characterization of intact proteins. Electron-based activation methods, including electron capture dissociation (ECD) and electron transfer dissociation (ETD), use exothermic electron transfer reactions to induce fragmentation, predominantly yielding c/z ions. Supplemental collision activation or infrared photoactivation coupled to ECD or ETD (generally known as activated ion ECD or ETD) enhanced the fragmentation efficiency of the electron-based methods by converting non-dissociated precursors into assignable fragment ions. Photodissociation, particularly ultraviolet photodissociation (UVPD), utilizes high-energy photons to activate precursor ions. UV photons are readily absorbed by amide chromophores of the protein backbone, offering substantial energy deposition and causing fragmentation without significant dependence on precursor charge state or primary sequence. For proteins, UVPD favors production of a/x fragment ions along with lower abundances of b/y and c/z ions, sometimes occurring with hydrogen migrations that result in additional a+1, x+1, and y-1 fragment ions as well as y-2 fragment specific to proline residues. For the most confident assignment of fragment ions in MS/MS spectra of intact proteins, fragment ions are evaluated with high mass accuracy (low ppm error tolerance) and matched to isotope patterns generated for the theoretical molecular compositions. Manual interpretation of the resulting fragment ions is time consuming, making automated identification and validation of fragment ions necessary. The earliest automated workflows for identification of fragment ions utilized spectral deconvolution prior to fragment identification. This processing step reduces spectral complexity by 'de-charging' and often 'de-isotoping' m/z domain data, resulting in a list of monoisotopic masses and their composite abundances which significantly simplifies downstream identification. Deconvolution algorithms applied to high resolution data frequently generate these monoisotopic masses via identification of well-delineated isotopic distributions in the m/z domain and assign the charge states by isotope spacing. In mass spectra of proteins, the monoisotopic mass is often generated based on the isotopic distribution and the 'averagine' model, a composite, average amino acid chemical formula weighted by the prevalence of each amino acid in the proteome. This approach enables rapid and accurate conversion of m/z domain data to mass domain data, which has been leveraged by several software approaches for the successful annotation of protein MS/MS spectra, including ProSight Lite, TopPIC, and our own MS-TAFI. Other software approaches have introduced workflows enabling identification of fragment ions directly in the m/z domain without deconvolution, including ProSight Native, TDValidator, MASH Suite, and ExD Viewer. Identification of fragment ions directly in the m/z domain based on their isotopic distributions without prior deconvolution is a complex task; however, modern approaches are increasingly implementing fragment ion searches in this manner. The advantage inherent in this approach is in direct observation of the abundances of each charge state and the observed isotopic masses. Furthermore, incorporation of heteroatoms or an amino acid composition that deviates from the averagine isotope table can be more readily considered when modelling fragment ion isotopic distributions. For example, a common heteroatom is sulfur, where averagine tables with and without cysteine and methionine residues are applied depending on the expected sulfur content of the protein. To facilitate more widespread adoption of fragment identification in the m/z domain rather than the deconvoluted mass domain in top-down proteomics, we have developed Proteo-SAFARI, an R Shiny application for the identification of protein fragment ions in top-down MS/MS spectra. This workflow can be readily applied to top-down MS/MS spectra of proteins collected on Orbitrap platforms processed using the 'export' function available in Xcalibur. Additionally, this approach is optimized for UVPD data, where overlapping fragment ions species containing hydrogen shifts can be quantified using a nonnegative least squares regression model for accurate assessment of the observed isotopic distributions. To showcase the utility of this application, we apply Proteo-SAFARI to top-down data of various benchmark proteins. We also consider proteins in low charge states, as demonstrated for ubiquitin charge reduced during the electrospray process to the 1+ charge state.