The emerging field of phyloproteomics seeks to categorize the relationships between microorganisms by the mass of their respective proteins. Now researchers at the University of Maryland in College Park have used matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to obtain protein biomarkers from fungal cells that they compared with those in genome and protein databases, illustrating the potential of the technique to identify unknown fungi.MALDI-TOF mass spectrometry has a number of promising applications in human and veterinary medicine as well as in environmental monitoring. It can distinguish cancerous from normal cells, manage bovine spongiform encephalitis, and identify and track parasites that can render breeding cows infertile. It also may enable rapid water and air testing and the characterization of sporulating bacteria such as anthrax. The technique's potential for the identification of fungi, however, remains to be fully explored.The researchers analyzed samples of Candida albicans, Saccharomyces cerevisiae and Epidermophyton floccosum using a MALDI 4 TOF mass spectrometer from Kratos Analytical Inc. of Chestnut Ridge, N.Y. The instrument was outfitted with a 337-nm, adjustable-power laser for ultraviolet sampling. They used six matrices in the experiments to determine the most suitable for this application.They found that the technique yielded distinctive spectra for the different organisms and that a sinapic acid matrix offered the highest-quality spectra. To identify the proteins, they entered the average masses of the derived spectral peaks into the Sequence Retrieval System module in SwissProt/Trembl from the Swiss Institute of Bioinformatics in Geneva.Other methods -- including culturing the cells and examining their morphology and biochemistry, and interrogating the cells with polymerase chain reaction -- can identify fungi. The latter, however, takes roughly an hour."The advantage of mass spectrometry is that the analysis takes less than two minutes," said Catherine Fenselau, a professor in the department of chemistry and biochemistry at the university who worked on the project.Fenselau cautioned, however, that it is not yet clear whether the information provided by mass spectrometry is as definitive as that by polymerase chain reaction.Overcoming obstaclesPeter Leopold, president of BioAnalyte Inc. in Portland, Maine, which develops tools for MALDI-TOF mass spectrometry profiling, believes that the obstacles to the widespread deployment of the technique are less technological than economic. It remains capital-intensive, and less expensive methods can do the same job.When its cost eventually comes down, however, MALDI-TOF will become more appealing, particularly for industries such as food safety, he predicted.Attention from the Food and Drug Administration or another crisis such as the mad cow epidemic also could precipitate its wider adoption.