The ‘top-down' proteomics approach utilizes molecular and fragment ion mass data obtained by ionizing and dissociating a protein in the mass spectrometer for the characterization of protein sequences and post-translational modifications. The topdown data are far more specific than the more widely used ‘bottom-up' approach. False-positive rates for the identification of proteins are lower with the top-down approach, and quantitation of multiply modified isomers is more efficient.

This report is concerned with the structural characterization of a protein, e.g., identifying and locating post-translational modifications or errors in the predicted sequence. The ‘top-down' methodology can directly subject a mixture of proteins, even of >10 components to yield a spectrum of their molecular ions that indicates the molecular mass values of individual proteins. MS MS of the mass-selected ions of a protein then provides fragment mass values for its structural characterization.

The top-down approach may be the method of choice for quantitation of position isomers of proteins containing multiple modifications.

In previous communications we reported MALDI, 'bottom-up' approach yielding biomarkers of colorectal carcinoma, competent embryos, proteomic changes in acute stroke and retinoic acid treated breast cancer cells. This report details and compares those results with data obtained from a 12 T Brucker Fourier Transform mass spectrometer (FTMS) with the same samples, and additional samples from placentas of smokers and non-smokers and breast cancers treated with caffeic acid and caffeic phenethyl ester. Sample preparation is by high pressure extraction (Barocycler) from tissue with ammonium bicarbonate buffer, and HPLC electrospray loading of the FTMS.