A recurring theme in proteomics is the demand for greater automation to increase efficiency and reproducibility. But to improve somebody's process, “you first have to convince them they've got one”, says John Hobbs, strategic market manager for Beckman Coulter in Fullerton, California. Beckman Coulter has modified and repositioned some of its products under the name ProteomeLab. The products are very “solutions-orientated”, says Hobbs. With the PF 2D automated, two-dimensional protein-fractionation system, for example, the company supplies the chemistry, the hardware, the software and the methods, and “we basically tell the customer don't mess with it”, he says. The PF 2D uses chromatofocusing followed by non-porous reverse-phase chromatography for high-resolution separation of proteins from complex mixtures. Fraction collection from the first dimension is controlled by an in-line pH monitor, with automatic injection of the fractions into the second dimension. Liquid fractions can be stored or the eluent connected directly to electrospray ionization–mass spectrometry. Beckman Coulter is working with mass spectrometer vendors to ensure compatibility with MALDI (matrix-assisted laser desorption/ionization) plate spotters.

Although non-gel-based methods coupled with mass spectrometry (MS) are gaining acceptance, the most commonly used approach is still a combination of two-dimensional gel electrophoresis (2DE) and MS. Two-dimensional gel electrophoresis is difficult to automate, but NextGen Sciences of Huntingdon, UK, will soon be shipping a fully automated 2DE platform — a2DE. Immobilized pH gradient strips (up to 30 cm) are run in parallel in the first dimension and three large-format SDS-PAGE gels in the second, and all steps between sample injection and SDS-PAGE are automated. Future versions will allow the same degree of optimization in the first dimension as currently offered in the second dimension, says chief executive Kevin Auton. Then “you can really start to zoom in on certain isoelectric points, as well as molecular-weight ranges”, he says.

For about US$2 million, Proteome Systems in North Ryde, Australia, sells a start-to-finish automated proteomics solution called ProteomIQ, launched last year — or you can buy the components separately. It comprises kits and instruments for sample preparation and protein separation, Shimadzu-Biotech's Axima CFR Plus MALDI-TOF (time-of-flight) mass spectrometer and bioinformatics capabilities. The Xcise gel-processing robot, developed jointly with Shimadzu-Biotech of Kyoto, Japan, bundles the functions of gel imaging, precision spot cutting, protein digestion and peptide purification, and deposition onto a target plate into one instrument. Also developed with Shimadzu-Biotech, the novel Chemical Inkjet Printer (ChIP) uses piezoelectric printing technology to dispense minute amounts of reagents onto selected protein spots electroblotted from 2D gels onto membranes. After processing, the membrane can be placed directly into the mass spectrometer for peptide analysis. ChIP not only cuts down on liquid-handling steps but also offers the option of archiving samples for future analysis.