Time-of-flights and traps: from the Histone Code to Mars

Abstract

Two very different analytical instruments are featured in this perspective paper on mass spectrometer design and development. The first instrument, based upon the curved-field reflectron developed in the Johns Hopkins Middle Atlantic Mass Spectrometry Laboratory, is a tandem time-of-flight mass spectrometer whose performance and practicality are illustrated by applications to a series of research projects addressing the acetylation, deacetylation and ADP-ribosylation of histone proteins. The chemical derivatization of lysine-rich, hyperacetylated histones as their deuteroacetylated analogs enables one to obtain an accurate quantitative assessment of the extent of acetylation at each site. Chemical acetylation of histone mixtures is also used to determine the lysine targets of sirtuins, an important class of histone deacetylases (HDACs), by replacing the deacetylated residues with biotin. Histone deacetylation by sirtuins requires the co-factor NAD+, as does the attachment of ADP-ribose. The second instrument, a low voltage and low power ion trap mass spectrometer known as the Mars Organic Mass Analyzer (MOMA), is a prototype for an instrument expected to be launched in 2018. Like the tandem mass spectrometer, it is also expected to have applicability to environmental and biological analyses and, ultimately, to clinical care.

Figure 1

Tandem time-of-flight mass spectrometer configurations utilizing the curved-field reflectron. (a) dual reflectron TOF described in Reference , (b) modified Kratos AXIMA CFR mass spectrometer, and (c) Shimadzu Biotech TOF² mass spectrometer.

Figure 2

Tandem TOF mass spectra of C60 fullerenes (a) obtained on the dual reflectron mass spectrometer and (b) obtained on the modified Kratos AXIMA CFR mass spectrometer.

Figure 3

The acetylation and deacetylation of histones.

Figure 4

Tandem TOF mass spectrum of a tryptic peptide from the HAT domain of p300/CBP.

Figure 5

MALDI/TOF mass spectrum of the histone H4_4–17 tryptic fragment following deuteroacetylation.

Figure 6

MALDI/TOF mass spectra of the tryptic digest of a mixture of histones (H1, H2a, H2b, H3 and h4) from calf thymus following acetylation, reaction with the deacetylase Hst and biotinylation, with and without cofactor NAD+.

Figure 7

MALDI mass spectra of the synthetic P12 peptide variant AARRPAGARRRAR (a) with cofactor NAD+ and (b) with Trypanosome bruceii Sirtuin TpSIR2 and cofactor NAD+.

Figure 8

(a) cross-sectional schematic of the MOMA ion trap mass spectrometer showing the location of the laser source, ion guide and electron source. (b) mass spectrum of the calibration compound PFTBA obtained on a prototype instrument.