At the less expensive end of the market is the ion-trap mass spectrometer, which is reasonably sensitive and has a reputation for being rugged, reliable and easy to use. But conventional three-dimensional ion traps have limited trap capacity, although newer instruments offer improvements on this front. The 1100 Series LC-MSD Trap XCT non-linear ion trap from Agilent in Palo Alto, California, for example, has a trap capacity four to eight times greater than its predecessor, which the company says will give a tenfold increase in sensitivity. Prices start at about US$200,000. The linear or two-dimensional ion-trap machines, such as the LTQ LC-MS/MSn from Thermo Finnigan in San Jose, California, are also configured to offer greater ion storage capacity.

The new 4000 Q TRAP LC-MS/MS system from Applied Biosystems in Foster City, California, and MDS Sciex in Concord, Canada, is a triple-quadrupole mass spectrometer where the last quadrupole can be operated as a conventional quadrupole mass filter or as a linear ion trap — an arrangement that allows decoupling of precursor ion isolation and fragmentation from the ion trap itself. The company says that this provides more sensitive tandem mass-spectrometry (MS/MS) and allows the identification and measurement of low levels of post-translational modification in a single liquid chromatography–MS/MS run. “This is one of the few instruments where you'd actually be able to do the protein identification work, protein characterization and absolute quantitation on the same instrument,” claims Ron Bonner, director of applied research at MDS Sciex.

At the top end of the market, Bruker Daltonics in Billerica, Massachusetts, and Thermo Finnigan have hybrid Fourier transform MS (FTMS) instruments. Bruker's APEX-Q analyses ions in the ion cyclotron resonance cell under high vacuum in a high magnetic field. Frank Laukien, president and chief executive of Bruker Daltonics, says that the hybrid 'front-end' for FTMS, high-field magnets (9.4 or 12 tesla) and COMPASS software are suitable for 'shotgun' proteomics as well as a 'top-down' approach that does not depend on enzymatic digestion as a precondition for protein-sequence analysis. The Finnigan LTQ-FT consists of a linear ion trap, a high-transmission ion-guidance system, and an ion cyclotron resonance analyser based on a 7-T superconducting magnet.

But the ultra-high resolution and greater mass accuracy of FTMS comes at a price. The APEX-Q (9 T model) starts at about $1.25 million and rises to $2 million for the top-of-the-range 12-T model. And FTMS instruments have a reputation for being tricky to operate, although Laukien says that “anybody who can run an ion trap or a Q-TOF can also run a FTMS”. Whether the enhanced analytical capability of these high-end instruments will offset their cost remains to be seen. John Yates of the Scripps Research Institute in La Jolla, California, believes it might. “I think these are going to have a huge impact if they wind up being user-friendly,” he says.