Proteomics is the study of proteins, particularly focused on examining ALL proteins in a fraction, cell, or tissue at the same time. Thus, for proteomics to be successful on a particular sample, one must identify all proteins, determine their modifications, and 3-D structure. Considering that the human cell has ~40,000 genes which can theoretically generate >100,000 proteins each of which can have one or more of >200 known post-translational modifications (ignoring mutations), this is an enormous analytical challenge.

The first parts of this challenge, identification of proteins and their modifications, can be addressed with mondern mass spectrometry instrumentation and methods, which has lead to a tremendous growth in the interest and need for high performance mass spectrometry instrumentation. The problem is in developing instrumentation that is simple enough for a biochemist to use, but without reducing the performance of the instrument.

Fourier transform mass spectrometry is the highest performance instrumentation available, but tends to be limited to use by experts due to the complexity of the data systems. Improvement in the instrumentation and data systems is thus required for acceptance of FTMS by the average biochemist.