Solutions for Top-Down Sequencing
Sequencing of protein N- and C-termini
MALDI-TDS efficiently reads out N- and C-terminal sequences even from large proteins (> 40 kDa) using the in-source decay fragmentation (ISD) in the MALDI source. These can be used to identify an unknown protein, to assign detailed structures of fusion proteins or mutation sites. Even complex, PEGylated therapeutic proteins can be analyzed using MALDI-TDS. Extending traditional Edman sequencing capabilities, MALDI-TDS works as well on N-terminally blocked proteins. MALDI-TDS is available on the 
ultraflex(-TOF/TOF) and the APEX ultra with ESI/MALDI dual source. On the ultraflex-TOF/TOF, fragmentation of glycopeptides using ISD provides selective readout of peptide sequences, whilst the classical CID process delivers preferentially glycan fragments.
Internal sequencing
Histones have been efficiently characterized using TDS on the HCT ultra. The ability to read out large parts of sequences from proteins <10 kDa after precursor ion selection of charge states 2-4. This permits histone characterization in mixtures without their previous chromatographic separation. An even increased mass range of proteins becomes accessible if ETD fragmentation is used after previous proton transfer reaction (PTR), which brings the higher charge states of larger protein fragments down to 2-4 - certainly compatible with ion trap analysis.
Mandatory for the complete characterization of undigested proteins (including precision MS, sequence determination and full detection of all modifications) is the extremely high resolution of an FT-ICR-MS, which permits fragment readouts on the sub-ppm scale at > 50 000 resolving power. The APEX ultra permits the isolation and fragmentation of individual proteins even from more complex mixtures for top-down sequencing and provides the option of selecting between the comprehensive ESI based ECD fragmentation with more exhaustive data treatment or the easy to read out, straightforward characterization by MALDI-TDS, which uses single charged ions only.
