Use of double-depleted ¹³C and ¹⁵N culture media for analysis of whole cell bacteria by MALDI time-of-flight and Fourier transform mass spectrometry

In the present paper, results demonstrating the significant advantages of matrix-assisted laser desorption/ionization (MALDI) analysis of whole cell samples of bacteria grown on double isotopically-depleted (13C and 15N) media are presented. It is shown that several advantages accrue for MALDI with a 9.4 T Fourier transform mass spectrometer (FTMS). Of particular note, for analysis of whole cells, sample preparation is simple and chemical interference is reduced. Moreover, ion coalescence problems are minimized, and data-base identification of proteins facilitated. Furthermore, high resolution mass spectra obtained from such whole cells show significant improvement in apparent mass resolving power and mass measurement accuracy, whether time-of-flight or FTMS MALDI is used. As a consequence, it becomes possible to detect subtle details in the chemistry of the organism, such as the presence of both post-translationally modified and unmodified versions of the same proteins. This approach is also adaptable to direct assay of over-expressed proteins from Escherichia coli cultures and should facilitate studies aimed at the detection of medically important cellular biomarker proteins.