Towards a second generation of ionic liquid matrices (ILMs) for MALDI-MS of Peptides, proteins, and carbohydrates

Second generation ionic liquid matrices are developed, examined, and tested. They have shown a wide mass detection range (<1000 Da to >270,000 Da) for proteins and peptides with greater S/N ratios than solid matrices. These ionic liquid matrices also exhibit the ability to effectively ionize proteins of large mass without disrupting noncovalent interactions between monomers. Both the anionic and cationic moieties have been varied systematically to find an ionic liquid matrix with the best physical properties, analyte signal intensity, and widest mass detection range. It was determined that both the proton affinity and pK_a of the cation have a large effect on the ionic liquid matrices’ ability to effectively ionize the analyte. The ionic liquid matrices can be used to detect polysaccharides with fewer degradation products than solid matrices. N,N-diisopropylethylammonium α-cyano-4-hydroxycinnamate and N-isopropyl-N-methyl-t-butylammonium α-cyano-4-hydroxycinnamate were the best matrices for proteins and peptides, while N,N-diisopropylethylammonium α-cyano-4-hydroxycinnamate and N,N-diisopropylethylammonium ferulate were the best matrices for carbohydrates.