Annotation and reannotation of bee genes. MS2 data were searched against a 6-frame translation of all ORFs from the honey bee genome, ignoring matches to contaminants, partial/non-tryptic, short (≤ 5 residues), and end-of-sequence peptides. Peptides that match already annotated proteins are in ➀, and those that did not are in ➁. In ➂, the ORFs matched by ➁ were compiled. In ➃, we tested which peptides can be matched to the ORFs in ➂. The ORFs which are matched only by peptides of ➁ are novel proteins (➄). The ORFs which are matched by peptides from both ➀ and ➁ are corrections of already annotated proteins (➅); most commonly, these were residues that had previously been falsely classified as introns, where current MS spectra now confirm their expression. "GROUP A" and "GROUP B" proteins refer to corrected and new proteins, respectively (see manuscript text).
Chan et al. BMC Genomics 2011 12:290 doi:10.1186/1471-2164-12-290