Drosophila　melanogaster　is　one　of　the　most　widely　used　model　organisms　in　life　sciences.　Mapping　its　proteome　is　of　great　significance　for　understanding　the　biological　characteristics　and　tissue　functions　of　this　species.　However,　the　comprehensive　coverage　of　its　proteome　remains　a　challenge.　Here,　we　describe　a　high-coverage　analysis　of　whole　fly　through　a　1D　gel　electrophoresis　and　LC-MS/MS　approach.　By　combining　the　datasets　of　two　types　of　SDS-PAGE　and　two　kinds　of　tagmata,　the　high-coverage　analysis　resulted　in　the　identification　of　5262　genes,　which　correspond　to　38.23%　of　the　entire　coding　genes.　Moreover,　we　found　that　the　fly　head　and　body　have　different　molecular　weight　distributions　of　their　proteomes　when　the　proteins　were　resolved　with　SDS-PAGE　and　image　analysis　of　the　stained　gel.　This　phenomenon　was　further　confirmed　by　both　label-free　and　isobaric　tags　for　relative　and　absolute　quantitation-based　quantitative　approaches.　The　consistent　results　of　the　two　different　quantitation　methods　also　demonstrated　the　stability　and　accuracy　of　the　LC-MS/MS　platform.　The　MS　proteomics　data　have　been　deposited　to　the　ProteomeXchange　with　identifiers　PXD000454　and　PXD000455　(http://proteomecentral.proteomexchange.org/dataset/PXD000454;　(http://proteomecentral.proteomexchange.org/dataset/PXD000455).