Proteo-SAFARI: An R Application for Identification of Fragment Ions in Top-Down MS/MS Spectra of Proteins.

Proteo-SAFARI is a shiny application for fragment assignment by relative isotopes, an R-based software application designed for identification of protein fragment ions directly in the m/z domain. This program provides an open-source, user-friendly application for identification of fragment ions from a candidate protein sequence with support for custom covalent modifications and various visualizations of identified fragments. Additionally, Proteo-SAFARI includes a nonnegative least-squares fitting approach to determine the contributions of various hydrogen shifted fragment ions (a + 1, x + 1, y - 1, y - 2) observed in UVPD mass spectra which exhibit overlapping isotopic distributions. To show its utility, Proteo-SAFARI is applied to various MS/MS spectra of intact proteins, including proteins exhibiting dynamic hydrogen shifts in y ions, ubiquitin charge-reduced to the 1+ charge state, and a large protein recorded in full profile mode. Proteo-SAFARI is available at: github.com/mblanzillotti/Proteo-SAFARI.