Chan et al. BMC Genomics 2011, 12:290 http://www.biomedcentral.com/1471-2164/12/290 Page 8 of 11 a b Figure 7 Example of a corrected protein sequence, using MS-detected peptide as evidence, with screenshots from the PeptideAtlas user interface. (I) The sequence of XP_392304.3, which is the current version available publicly, is interrupted by an apparent intron after residue 242. However, when searching MS data against a set of ORFs derived from six-frame translations of the bee genome, the peptide VQTVATPSIIER was found only 21 residues C-terminally from residue 242, within what was originally thought to be an intron. (II) Using the PeptideAtlas interface, one can visualize the location of the peptide (circled in red) with respect to the whole protein, (III) explore the frequency of observations of the peptide, and (IV) view the individual spectrum pertaining to each observation. Figure 7b. Example of a new protein, using MS-detected peptide as evidence, with screenshots from the PeptideAtlas user interface. (I) The sequence 110761371-2_148730 is an ORF that is not part of the annotated honey bee protein database, yet is matched by three unique peptides. Clicking on any peptide, for example PAp01422113 (circled in red), reveals the sequence itself (LNSPPTPTTSTPTFR - see II), the frequency of observations and more precisely, the samples that contain the peptide spectrum. (III) After clicking on the spectrum icon for any of the samples, the relevant spectrum is shown.