GUMBOS matrices of variable hydrophobicity for matrix-assisted laser desorption/ionization mass spectrometry Hashim Al Ghafly, Noureen Siraj, Susmita Das, Bishnu P. Regmi, Paul K. S. Magut, Waduge Indika S. Galpothdeniya, Kermit K. Murray* and Isiah M. Warner* Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA RATIONALE: Detection of hydrophobic peptides remains a major obstacle for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This stems from the fact that most matrices for MALDI are hydrophilic and therefore have low affinities for hydrophobic peptides. Herein, 1-aminopyrene (AP) and AP-derived group of uniform materials based on organic salts (GUMBOS) as novel matrices for MALDI-MS analyses of peptides were investigated for hydrophobic and hydrophilic peptides. METHODS: A number of solid-phase AP-based GUMBOS are synthesized with variable hydrophobicity simply by changing the counterions. Structures were confirmed by use of 1 H NMR and electrospray ionization mass spectrometry (ESI-MS). 1-Octanol/water partition coefficients (K o/w ) were used to measure the hydrophobicity of the matrices. A dried-droplet method was used for sample preparation. All spectra were obtained using a MALDI-TOF mass spectrometer in positive ion reflectron mode. RESULTS: A series of AP-based GUMBOS was synthesized including [AP][chloride] ([AP][Cl]), [AP][ascorbate] ([AP][Asc]) and [AP][bis(trifluoromethane)sulfonimide] ([AP][NTf 2 ]). The relative hydrophobicities of these compounds and α-cyano- 4-hydroxycinnamic acid (CHCA, a common MALDI matrix) indicated that AP-based GUMBOS can be tuned to be much more hydrophobic than CHCA. A clear trend is observed between the signal intensities of hydrophobic peptides and hydrophobicity of the matrix. CONCLUSIONS: MALDI matrices of GUMBOS with tunable hydrophobicities are easily obtained simply by varying the counterion. We have found that hydrophobic matrix materials are very effective for MALDI determination of hydrophobic peptides and, similarly, the more hydrophilic peptides displayed greater intensity in the more hydrophilic matrix. Copyright © 2014 John Wiley & Sons, Ltd. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is an important tool for the rapid and sensitive analyses of biomolecules. [1] In MALDI analysis, the matrix is an essential component, and selection of a suitable matrix is critically important because the optimal performance of many matrices has been found to depend on the chemical characteristics of the analyte. [2–4] Therefore, there have been intense efforts towards development and evaluation of novel and effective matrices for MALDI-MS analyses of different analytes. [5–17] In general, MALDI matrices must possess specific properties that include, but are not limited to, strong absorption of laser radiation, ability to effectively disperse analytes, good miscibility with the solvent and analytes, efficient energy transfer to analyte for ionization and desorption, ability to serve as a good protonating and deprotonating agent, and also vacuum stability. [9] The majority of MALDI matrices studied so far possess hydrophilic characteristics, which are particularly well suited for detection of hydrophilic biomolecules. [17,18] However, detection of hydrophobic biomolecules remains an elusive limitation for MALDI analyses. This stems from the fact that hydrophilic matrices exhibit low affinities for hydrophobic biomolecules. It must be emphasized that a protein contains both hydrophilic and hydrophobic residues, and hence it is critical to also analyze hydrophobic peptides. [17,19] An additional problem in the analyses of hydrophobic peptides is their limited solubility in commonly used solvents for MALDI-MS. To overcome this limitation, detergents have been employed to solubilize hydrophobic peptides in aqueous media. [17] These detergents, being amphiphilic, improve the solubility of hydrophobic proteins. However, use of surfactants at critical micelle concentrations can cause deterioration of the spectral quality of peptides, yielding poor signal-to-noise ratios, as well as poor mass resolution. [17,20] Despite several attempts to develop new matrices for hydrophobic peptides and proteins, [16,19,21–26] limited success has been achieved in MALDI detection of hydrophobic biomolecules. For this reason, synthesis and evaluation of new matrices are still a priority for selective detection of hydrophobic biomolecules within complex biological samples. It has been observed that it is simple to detect hydrophobic biomolecules with hydrophobic matrices since * Correspondence to: K. K. Murray and I. M. Warner, Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA. E-mail: kkmurray@lsu.edu; iwarner@lsu.edu Copyright © 2014 John Wiley & Sons, Ltd. Rapid Commun. Mass Spectrom. 2014, 28, 2307–2314 Research Article Received: 1 July 2014 Revised: 19 August 2014 Accepted: 24 August 2014 Published online in Wiley Online Library Rapid Commun. Mass Spectrom. 2014, 28, 2307–2314 (wileyonlinelibrary.com) DOI: 10.1002/rcm.7027 2307