Fig. 3
Top-down analysis using high precursor mass window searches identifies processing of the plastid ribosomal proteins. a For the plastid-specific ribosomal proteins (PSRPs) of the chloroplastic 70S ribosome, the translation factor pY and the ribosome recycling factor (RRF), several co-occurring proteoforms could be identified and quantified, resulting from post-translational modification and/or processing of the termini. In the corresponding cryo-EM structure of the chloroplastic 70S ribosome, RRF was not modelled due to absence of electron density14. b, c The chloroplastic ribosomal protein L27 is processed at both the N- and C-terminus and is therefore not detected through top-down sequencing when searching for the intact gene product. Corrections to either the N- or C-terminal sequence provides fragment ions from the C- and N-terminus, respectively, as long as the precursor mass window is larger than the mass of the sequence correction. d, e In a similar way, variable processing at the N-terminus of the chloroplastic ribosomal protein S6 could be detected by using C-terminal fragments to first identify which intact masses belong to S6 and subsequently correct the sequence until the theoretical and measured masses matched
