Two-dimensional partial covariance mass spectrometry for the top-down analysis of intact proteins

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 parent ion. The technique has been applied so far to peptides and oligonucleotides. 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 biomolecular sequence than 1D MS/MS signals at a given 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. 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 multiple intact protein ions from the same fragment ion spectrum.