Proteo-SAFARI

Proteo-SAFARI identifies protein fragment ions directly in the m/z domain from top-down MS/MS spectra using fragment assignment by relative isotopes.

Key Features:

• Fragment ion assignment: Identifies fragment ions from a candidate protein sequence with support for custom covalent modifications.
• Visualization: Provides various visualizations of identified fragments.
• Hydrogen-shifted fragment ion fitting: Uses nonnegative least-squares fitting to determine contributions of hydrogen-shifted fragment ions (a + 1, x + 1, y - 1, y - 2) with overlapping isotopic distributions observed in UVPD mass spectra.

Scientific Applications:

• Intact protein MS/MS analysis: Applied to 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.
• UVPD mass spectra interpretation: Enables analysis of hydrogen-shifted fragment ions with overlapping isotopic distributions in ultraviolet photodissociation data.

Methodology:

Fragment assignment by relative isotopes with nonnegative least-squares fitting for hydrogen-shifted fragment ion contributions.