An integrated microsystem providing rapid analyses of trace-level tryptic digests for proteomics application is presented. This modular microsystem includes an autosampler and a microfabricated device comprising a sample introduction port and an array of separation channels together with a low dead-volume facilitating the interface to nanoelectrospray mass spectrometry. Sequential injection and separation of peptide standards and tryptic digests was achieved with a throughput of up to 30 samples per hour with less than 3% sample carryover. Replicate injections of peptide mixtures indicated that reproducibility of migration time was typically better than 2.3% relative standard deviation (RSD) whereas RSD values of 3.7-11.8% were observed on peak height. Mass spectral detection of submicromolar protein digests (< 7 femtomoles/injection) was achieved using a quadrupole/time of flight instrument in less than 2 min/per sample with peak widths of 1.8-7.0 s. The analytical potential of this integrated device for the identification of gel isolated proteins from Neisseria meningitidis immunotype L3 has been demonstrated using both peptide mass-fingerprint database searching and on-line tandem mass spectrometry.