In the June 2006 issue of BioTechniques, Thomas Conrads and colleagues wrote an article about mass spectrometry used in biomarker discovery . It is part of a “Special Section” devoted to mass spectrometry for proteomics analysis that is worth reading in itself. But one figure caught my attention. In this figure (reproduced below), they plot the mass spectrometry data acquisition effort and bioinformatic effort -vs- the experimental focus. In the few past years, people relied too much on the increasing power of mass spectrometry and bioinformatic tools in their experimental design. The authors criticise the fact that people “are overly dependent on technology and suffer from lack of imaginative sample preparation”. It’s not because analysis power is available downstream that sample collection and processing could be neglected.
Reproduction of Conrads’figure 1
As shown in Figure 1, there is often an inverse relationship between the complexity of sample preparation and the amount of data acquired or the sophistication of the bioinformatic analysis. Simply put, minimal sample preparation prior to MS analysis will require more data acquisition and more sophisticated bioinformatic analysis. There is, however, a direct correlation between the amount of data acquired and the sophistication of the bioinformatic analysis.
Schematic protein identification process (for those who need it)
 T.P. Conrads, B.L. Hood and T.D. Veenstra. Sampling and analytical strategies for biomarker discovery using mass spectrometry. BioTechniques (June 2006) 40 (6): 799-805 (full text in html ; free registration required)