A microcapillary column switching HPLC-electrospray ionization MS system for the direct identification of peptides presented by major histocompatibility complex class I molecules.

A microcapillary column switching high-performance liquid chromatography (HPLC) system was developed for the separation of major histocompatibility complex (MHC) class I associated peptides. Combination of the column switching system with electrospray ionization mass spectrometry (ESIMS) enabled the detection and identification of the peptides at low-femtomole levels. Sample volumes of 30-50 microL were injected and concentrated onto a short, 100-micron-i.d. precolumn. The precolumn was coupled to a 100-micron-i.d. reversed-phase analytical HPLC column via a six-port valve. Peptides were separated on the analytical column using an ESI-compatible mobile phase at a flow rate of 0.5 microL/min. Peptides were eluted directly into the ESI source of either a magnetic sector MS or an ion trap MS. Peptides associated with human leukocyte antigen A*0201 molecules were determined in immunoaffinity-purified extracts from either measles virus infected cells or uninfected cells by microcapillary column switching HPLC-ESIMS. The approach toward detection of virus-specific peptides we used was based on the comparison of ion chromatograms obtained from the LC-MS analysis of extracts from virally infected cells and their uninfected counterparts. In this way, the molecular mass of peptides unique to virus infected cells was obtained. The utility of the system is demonstrated by the identification of a candidate epitope. Microcapillary column switching HPLC was used along with ESI ion trap tandem MS to identify the naturally processed viral peptide KLWESPQEI. This peptide was found to derive from the measles virus nonstructural protein C. The approach described here provides a versatile and sensitive method for the direct identification of viral peptides associated with MHC class I molecules.