High-sensitivity analysis and sequencing of peptides and proteins by quadrupole ion trap mass spectrometry

This paper describes experience with the commercially available LCQ quadrup ole ion trap mass spectrometer applied to the off-line analysis of peptides and proteins. The standard front end of the electrospray probe was replace d with a micromanipulator which, with the aid of a magnifying device, allow ed the use of a variety of miniaturized spraying interfaces. The low sample consumption and extended analysis times of these devices were ideally suit able to obtain improved results in terms of sensitivity and mass accuracy. This needed a careful optimization of the number of ions stored inside the trap (ion target parameter) and required spectrum averaging of many scans. A method is presented for the mathematical fitting of ZoomScan spectra to t heoretical isotopic distributions, which allowed the mass determination of large peptides with more accuracy than that achieved by conventional deconv olution algorithms. A very simple on-line desalting configuration is also d escribed which needed no external micro-high-performance liquid chromatogra phic pumps, and can be easily mounted using the built-in syringe delivery s ystem of the LCQ. This set-up allowed extended analysis times of 'in-gel' p rotein digests in subpicomole amounts. Finally, the multiple fragmentation capabilities of the ion trap were found to be extremely useful for the anal ysis of peptide modifications such as phosphorylation and for sequencing in dividual peptides from highly complex MHC-bound peptide pools. Copyright (C ) 1999 John Whey & Sons, Ltd.