  Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the
inherent fluctuations of fragment ion abundances across a series of tandem mass
spectra, to identify correlated pairs of fragment ions produced along the same
fragmentation pathway of the same parent (e.g. peptide) ion. Here, we apply
2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap
mass analyzer, using the fact that the fragment-fragment correlation signals
are much more specific to bio-molecular sequence than 1D MS/MS signals at the
same mass accuracy and resolution. We show that from the distribution of
signals on a 2D-PC-MS map it is possible to extract the charge state of both
parent and fragment ions without resolving the isotopic envelope. Furthermore,
the 2D map of fragment-fragment correlations naturally reveals the secondary
decomposition pathways of the fragment ions. We access this spectral
information using an adapted version of the Hough transform. We demonstrate the
successful identification of highly charged, intact protein molecules without
the need for high mass resolution. Using this technique we also perform the in
silico deconvolution of the overlapping fragment ion signals from two
co-isolated and co-fragmented intact protein molecules, demonstrating a viable
new method for the concurrent mass spectrometric identification of a mixture of
intact protein ions from the same fragment ion spectrum.
