**2.6.5 Advanced protein characterization with ESI-LC-MS and MALDI-TOF**

MALDI-TOF MS provides an ideal high-throughput solution for protein identification; however, where protein identity is ambiguous, known databases must be searched with a higher degree of sequence information. The Micromass Q-Tof family of MS-MS instruments incorporates quadrupole/ orthogonal acceleration time-of-flight (Q/oa-TOF) technology, enabling exact mass measurement, and acquisition of the highest-level peptide sequence information for de novo sequencing and BLAST analyses. Protein digest samples in microtiter plates, prepared with the Mass*PREP* station, can be transferred directly to the Micromass CapLC (capillary HPLC) system for automated injection into the Q-Tof *micro* for integrated LC-MS-MS under MassLynx software control. The capability for MS to MS-MS switching "on the fly" with the Q-Tof family of instruments maximizes the amount of amino acid sequence information that can be generated with these instruments. MassSeq software also provides the capacity for automated de novo amino acid sequencing based on the MS results.
