To fully automate the sample introduction step for nanoscale microcapillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses, 75 microm i.d. x 14 cm capillary columns were interfaced with a commercial autosampler instrument using a novel procedure which allowed dilute peptide samples to be transferred from the AS loop injector to the nanoscale column at flow rates up to 5 microL min(-1). On-column enrichment and desalting was demonstrated for large sample volumes (>40 microL) by constructing a vent 2 cm after the entrance to the packed bed of 5-microm ODS-AQ modified silica. Salts and nonretained solutes were removed via the vent, which allowed for column washing independent of the continuation of the bed into the electrospray source. Separations of test peptide mixtures demonstrated 50-nL elution peak volumes with low- to subfemtomole detection levels. In addition, a highly complex peptide mixture (outer membrane preparation from Psuedemonas aeruginosa) was efficiently separated with more than 100 proteins identified from a single reversed-phase LC-MS/MS analysis. Finally, the vented column (V-column) was utilized for on-line separations in a multidimensional chromatography/tandem MS experiment where large numbers of strong cation exchange chromatography fractions from a trypsinized yeast lysate were desalted, concentrated, and analyzed in a completely automated fashion. The procedures for constructing and using a V-column require minimal changes in current methods and equipment for nano-LC-MS analyses using columns of 100-microm diameter and smaller.
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