Toward a complete LC-MS mapping system for peptides and proteins, we have coupled a precision-flow microbore HPLC system to an electrospray single quadrupole mass spectrometer. The HPLC system allows fast separation of protein digests with UV detection at the low pmol level. A 2 microliters/min portion (1:25) of the effluent is passed into a high-sensitivity electrospray MS system. The electrospray source allows for molecular mass associated ions (MH+, MH2(2+), MH3(3+), etc.) to be generated as well as collision induced dissociation of these ions before MS analysis. After LC-MS runs, with or without partial fragmentation, the data generated are largely interpreted by identification of predicted peptides, incompletely digested peptides, unusual peptide cleavages, and so on, using appropriate integrated software (PEPMAP, PEPMATCH). Examples of peptide mapping at the low pmol level using this integrated system will be shown (e.g., of the protein human growth hormone and of the glycoprotein, tissue plasminogen activator).