Metabolic labelling techniques have recently become popular tools for the quantitative profiling of proteomes. Classical Stable Isotope Labelling with Amino acids in Cell cultures (SILAC) employs pairs of heavy/light isotopic forms of amino acids to introduce predictable mass differences in protein samples to be compared. After proteolysis, pairs of cognate precursor peptides can be correlated and their intensities used for mass spectrometry-based relative protein quantification. We present an alternative SILAC approach by which two cell cultures are grown in media containing isobaric forms of amino acids, labelled either with 13C on the carbonyl (C1) carbon or 15N on backbone nitrogen. Labelled peptides from both samples have the same nominal mass and nearly identical MS/MS spectra, but generate upon fragmentation distinct immonium ions separated by 1 u. When labelled protein samples are mixed, the intensities of these immonium ions can be used for the relative quantification of the parent proteins. We validated the labelling of cellular proteins with valine, isoleucine and leucine, with coverage of 97% of all tryptic peptides. We improved the sensitivity for the detection of the quantification ions on a pulsing instrument by employing a specific fast scan event. The analysis of a protein mixture with a known heavy/light ratio showed reliable quantification. Finally, the application of the technique to the analysis of two melanoma cell lines yielded quantitative data consistent with those obtained by a classical 2D-DIGE analysis of the same samples. Our method combines the features of the SILAC technique with the advantages of isobaric labelling schemes like iTRAQ. We discuss advantages and disadvantages of ISIS technique as well as possible ways to improve it.