The method of the invention provides novel compounds, termed acid-labile
isotope-coded extractants (ALICE), for quantitative
mass spectrometric analysis of
protein mixtures. The compounds contain a
thiol-reactive group that is used to capture
cysteine-containing peptides from all
peptide mixtures, an acid-labile
linker, and a non-biological
polymer. One of the two acid-labile linkers is isotopically labeled and therefore enables the direct quantitation of peptides / proteins through
mass spectrometric analysis. Because no functional proteins are required to capture peptides, a higher percentage of
organic solvent can be used to solubilize the peptides, particularly hydrophobic peptides, through the binding, washing and eluting steps, thus permitting much better
recovery of peptides. Moreover, since the peptides are covalently linked to the non-biological
polymer (ALICE), more stringent washing is allowed in order to completely remove non-specifically bound species. Finally, peptides captured by ALICE are readily eluted from the
polymer support under mild acidic condition with high yield and permit the direct down
stream mass spectrometric analysis without any further sample manipulation. In combination with our novel
dual column two dimensional liquid
chromatography-
mass spectrometry (2D-LC-MS / MS) design, the ALICE procedure proves to a general approach for quantitative
mass spectrometric analysis of
protein mixtures with better
dynamic range and sensitivity.