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Abstract Optimization of a matrix-assisted laser desorption ionization-ion mobility-surface-induced dissociation-o-time-of-flight mass spectrometer for peptide sequencing is discussed. Surface-induced dissociation (SID) spectra obtained by using stainless steel, Au grids, and fluorinated self-assembled monolayers (F-SAM) on Au are compared. The F-SAM surfaces yield similar fragment ions to those obtained using an adventitious hydrocarbon coated stainless steel surface; however, optimum collision energies differ for the two surfaces. The advantage of ion mobility-time-of-flight (TOF) is the ability to simultaneously acquire MS1 and MS2 spectra, which greatly facilitates high-throughput sequencing of peptides and mixtures of peptides resulting form the proteolytic digest of proteins. Simultaneous acquisition of ion mobility and TOF spectra introduces a time element to SID experiments that can be used as a probe of ion/surface interactions. Author Keywords: Matrix-assisted laser desorption; Time-of-flight; Orthogonal

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