The discovery stage of proteome profiling typically involves the comparison of different states of a cell or tissue. One approach utilizes fractionation of the proteome into intact proteins followed by mass spectrometry (MS). A two-dimensional, liquid chromatographic fractionation system, the ProteomeLab™ PF 2D, followed by a 3rd-dimension with MALDI-TOF MS has been used for this approach. The 1st-dimension separation is chromatofocusing where proteins are separated by pI and collected in fractions based on pH intervals. Upwards of 20 pI fractions are then separated in a 2nd-dimension by reversed-phase chromatography.