The major bottleneck of proteomics is no longer the ability to generate data, but the correct analysis of
proteomics data, and mining as much information from it as possible. This new software allows us to rapidly
analyze data generated by mass spectrometry in an extensive maner using advanced charge state
determination of MS spectra, search spectra using multiple search engines, data recombination, advanced
protein redundancy removal, unique post-process quatitation and iterative search methods to solve this
problem. We can typically expand the number of proteins identified by a factor of3-4 and number of pep tides
identified by the same. This allows us to now identify proteins with increased robustness and accuracy, mine
MS data for additional proteins and/or protein coverage using a process of iterative searching, and allow for
the more rapid identification of post-translational modifications, protein isoforms and potential
polymorphorisms. This softare also provides a list of additional targets for real-time data acquisition
decisions to increase ability to obtain additional MS data to fuher support and validate data.
