Top-down proteomics reveals novel protein forms expressed in methanosarcina acetivorans

Combining our previous work with current platforms presented here that identified 99 new proteins (Supplemental Table 1), a total of 200 protein identities in M. acetivorans have been confirmed. Of these, five proteins were unannotated, 15 were mispredicted, two exhibited variable removal of the start methionine, and one was a proteolysis fragment from the identical C-terminus of two possible proteins. The incorporation of LC-MS/MS and offline automation speeds up the processing of samples through automation of the top-down process. For five data files that were automatically processed and iteratively searched, 2 h were required to complete analysis. In these, a total of 835 identifications were detected by the search algorithm in this time period. The expanded use of top-down will use both online and offline strategies, with increasingly sophisticated data acquisition strategies tailored for the challenges of top-down fragmentation 16], 18], 19], 32] and 33]].