Abstract: In order to better understand the pathogenicity of respiratory viruses, we have used mass spectrometry based techniques to characterize sequence variations in the virus genome and to discover host proteins that interact with viruses. In the genomics method, virus genome regions between 300 and 800 bases in length were amplified by RT-PCR, followed by in vitro transcription with dU instead of rU or dC instead of rC. The transcription products were then digested with RNase A. Such strategy generated base-specific cleavage products that were ideal for MALDI mass spectrometric analysis. Any single point mutation could be identified by corresponding peak disappearance and appearance of other fragment(s). The method can be used for high-throughput comparative sequencing of virus genome. In the proteomics method, virus particles were purified from their host cells with sucrose gradient. The virus and interacting host cell proteins were solublized in SBS, immobilized and purified in polyacrylamide gel matrix, and then digested in gel. The peptide mixture were extracted and analyzed with nano-LCMS/MS. Host cell proteins were identified along with known virus proteins after database search and statistical analysis with Trans Proteomic Pipeline. Several host cell proteins identified with the proteomic approach were further validated with different biochemical assays.