Top‐down proteomics with a quadrupole time‐of‐flight mass spectrometer and collision‐induced dissociation

With slight modifications of the instrumental parameters, we demonstrate that satisfactory top‐down data can be obtained with collision‐induced dissociation (CID) tandem mass spectrometry on a quadrupole time‐of‐flight (qTOF) instrument not originally designed for this purpose. Protein identification is achieved with both N‐ and C‐terminal sequence tags and BLAST database searches. The accurate mass measurement of multiply charged fragment ions (mostly y and b‐type) supplements the limited set of cleavage sites and provides a high degree of sequence coverage (90–100%). Post‐translational modification issues can be addressed too. This approach might help those mass spectrometry (MS) core facilities that are not able to afford very high‐resolution instruments, thus expanding the benefits of top‐down protein analysis over the worldwide MS community. Copyright © 2009 John Wiley & Sons, Ltd.