Our lab also contains a Micromass Q-TOF instrument with a nanospray source. For peptides of up to approximately 5 kDa, this instrument has similar sample requirements and similar or better resolution as the MALDI-TOF instrument, with the added advantage that MS/MS experiments can be performed with great accuracy in order to conveniently obtain sequence information about the peptides, or to obtain detailed information about posttranslational modifications. Peptides derived from proteolytic digestion of proteins by trypsin are particularly suitable for sequencing by Q-TOF MS, largely because of the size of these peptides (often between 800 and 2500 Da) and because these peptides contain the basic amino acids lysine or arginine at their C-termini. Sequences of up to 30 amino acids can be obtained in this way. Our nanoflow source allows mixtures of peptides, for example from a tryptic digest of a protein from an SDS-PAGE gel, to be infused slowly into the instrument and the sequences from several peptides (up to 40 or more) can be obtained in a single experiment. By coupling the Q-TOF directly to a Waters CapLC nanoflow HPLC system, we can sequence over 700 peptides in a single experiment. The isobaric amino acids leucine and isoleucine cannot be distinguished by this method of peptide sequencing.

MS/MS Spectrum of [Glu1] Fibrinopeptide B (Click here to enlarge)