Schematic illustration of the workflow. Cell nuclei from TGF-β1 stimulated HFL-1 cells were isolated and disrupted by sonication followed by ICAT labeling and trypsin digestion. The tryptic peptides were separated by strong cation exchange chromatography and the ICAT labeled (cysteine-containing) peptides were affinity purified on an avidin column. The captured fractions were split in two. Half of the material was analyzed by online ESI LC-MS/MS on a Qstar(R) Pulsar System and half of the material was analyzed in HPLC coupled to an off-line MALDI target fraction collector and analyzed on AB 4700 Proteomics Analyzer.