Fluorophore-assisted laser desorption/ionization-mass spectrometry (FALDI-MS)

•Direct analysis of fluorescently labeled peptides by LDI-MS is demonstrated for the first time.•Peptides labeled on their N-termini with rhodamine B were analyzed by FALDI MS and MS/MS without the addition of a matrix.•MS/MS spectra of fluorescently labeled peptides show exclusively a and b ion series enabling easier peptide sequencing.•FALDI-MS allows for selective ionization of the fluorescently labeled peptides in peptide mixtures.

The direct analysis of fluorescently labeled peptides by laser desorption/ionization-mass spectrometry (LDI-MS) is demonstrated for the first time. Peptides labeled on their N-termini with rhodamine B were analyzed by MS and tandem MS (MS/MS) using a recently developed visible-wavelength LDI-MS instrument. Labeling with a fluorescent dye leads to soft LDI of peptides in the absence of a matrix. The MS/MS spectra were simplified because only a and b rhodamine B-containing peptide fragment ions were observed, which allowed for easy spectral interpretation and de novo sequencing of peptides. In mixtures, the rhodamine B labeled peptides demonstrated a greater ionization efficiency, and therefore selectivity, compared to ionization of the unlabeled peptides. Additionally, FALDI-MS was used to directly analyze beta-amyloid peptides that were N-terminally labeled with the fluorophore HiLyte Fluor™ 555. The described FALDI-MS methodology provides a novel way to ionize and structurally characterize specifically labeled peptides.

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