Matrix-assisted laser desorption/ionization mass spectrometry of hydrophobic peptides

Hydrophobic peptides, especially those with acid-labile protecting groups, are difficult to characterize using mass spectrometric methods. We have developed a new procedure for matrix-assisted laser desorption/ionization time-of-flight (MALDI-TCF) mass spectrometric analysis of such samples. Hydrophobic peptides, which are insoluble in aqueous solutions, are dissolved in chloroform and combined with matrixes prepared in chloroform or chloroform/methanol solutions. The use of a common solvent for the matrix and the analyte improves the analyte isolation step in MALDI mass spectrometry, The lack of acidic solutions previously used for electrospray ionization or MALDI mass spectrometry of hydrophobic peptides extends this methodology to cyclic or protected hydrophobic peptides. Conventional peptide matrixes, such as 2,5-dihydroxybenzoic acid and sinapinic acid, as well as 3-indoleacrylic acid are shown to be suitable for hydrophobic peptides. Cyclic hydrophobic peptides and linear hydrophobic peptides with blocked termini are detected as the cation-adducted pseudomolecular ion due to the lack of suitable sites of protonation on the analyte.