Ionic liquid matrix-induced metastable decay of peptides and oligonucleotides and stabilization of phospholipids in MALDI FTMS analyses

Room-temperature ionic liquid matrices (ILMs) have recently been investigated for use in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and proven to be advantageous. Literature accounts of ILM performance for biological samples document increased sensitivity and ionization efficiency. These claims have been investigated here, and are supported for MALDI TOF applications to peptides, oligonucleotides, and phospholipids. Peptides and oligonucleotides however, do not behave in the same way when ILMs are used for MALDI FTMS. As reported here, with 3 tesla MALDI FTMS peptides and oligonucleotides fragment readily. These observations contrast with those found for MALDI time-of-flight mass spectrometry. Fragmentation is apparently slower than the time required to accelerate ions in a MALDI TOF mass spectrometer, but is readily observed by MALDI FTMS. Therefore, fragmentation of these molecules must occur on a relatively slow time scale. As trapping time is extended, increased fragmentation of peptides and oligonucleotides is seen. However, phospholipids do not fragment extensively. Furthermore, use of traditional solid matrices causes significant fragmentation for this category of compound but is suppressed by use of ILMs.