Combinatorial post-translational modifications (PTMs),
such as
those forming the so-called “histone code”, have been
linked to cell differentiation, embryonic development, cellular reprogramming,
aging, cancers, neurodegenerative disorders,etc.
Nevertheless, a reliable mass spectral analysis of the combinatorial
isomers represents a considerable challenge. The difficulty stems
from the incompleteness of information that could be generated by
the standard MS to differentiate cofragmented isomeric sequences in
their naturally occurring mixtures based on the fragment mass-to-charge
ratio and relative abundance information only. Here we show that fragment–fragment
correlations revealed by two-dimensional partial covariance mass spectrometry
(2D-PC-MS) allow one to solve the combinatorial PTM puzzles that cannot
be tackled by the standard MS as a matter of principle. We introduce
2D-PC-MS marker ion correlation approach and demonstrate experimentally
that it can provide the missing information enabling identification
of cofragmentated combinatorially modified isomers. Ourin
silicostudy shows that the marker ion correlations can be
used to unambiguously identify 5 times more cofragmented combinatorially
acetylated tryptic peptides and 3 times more combinatorially modified
Glu-C peptides of human histones than is possible using standard MS
methods.