W260 Nucleic Acids Research, 2006, Vol. 34, Web Server issue Micromass pkl format (*.pkl) and Mascot mgf format (*.mgf). For reliable interpretation of PTMs, we recom- mend users to input spectra with mass error tolerance <1 Da. (ii) Protein database. Protein database should be in fasta format (*.fasta) and contain 20 or less protein sequences because a large protein database may produce bulky false positive results. (iii) PTM database. MODi can consider the entire unimod PTMs published in http://www.unimod.org. In addi- tion, users can configure their tailored PTM list composed of selected unimod PTMs and user-defined PTMs. It is possible to save and load user-selected PTM lists. Parameters Users can adjust MODi parameters appropriately according to one’s experimental conditions. The parameters include max- imum number of missed cleavages, mass tolerance, precursor mass tolerance and enzymes used. In addition, users can ﬁne- tune MODi by ﬁtting advanced parameters such as offset minimum/maximum value per gap, tag chain discard rate, minimum normalized intensity to consider, peak selection window size and minimum/maximum peaks in a window. Users can save parameters on a local host to re-use them for later analysis. A more detailed description of each para- meter can be found in help pages of the MODi website. Output MODi outputs a unidta ﬁle (*.unidta) and a unidrawing ﬁle (*.unidrawing). To guarantee random access, each ﬁle has a tailing offset list which indicates ﬁle offsets of input spectra. The unidta ﬁle is a set of input spectra and the unidrawing ﬁle is an XML formatted ﬁle which contains interpretations of input spectra. MassPective MassPective has been developed to help users understand the interpretation from unidta and unidrawing ﬁles. MassPective is a graphical tool that displays MODi’s output in a user- friendly manner and helps users understand MODi’s output quickly. It shows each spectrum with ion-type annotation, candidate peptides for the spectrum, tag-chains for the can- didate peptides and possible PTM interpretations for the tag- chains using graphical user interface. In addition, it enables users to perform additional manual de novo sequencing so that a MODi’s partial interpretation can be manually annotated with additional sequencing information. Given a spectrum, MassPective displays MODi’s output in three tiled windows (candidate peptide list, detailed informa- tion, and spectrum windows) and a pop-up gap list window (Figure 2). Candidate peptide list window shows candidate peptides for the current spectrum and tag-chains of each can- didate peptide. By selecting a candidate peptide or a tag chain, a user can see useful information such as score, offset list or gap list in the detailed information window. If a user clicks a tag chain, a pop-up window showing gap list appears. Gap list window shows combinations of PTMs that may occur in each gap and their scores and a user can select an interpretation of each gap so that the corresponding annotation in the spectrum window can be displayed. Spectrum window displays the selected spectrum together with various annotations a user selects. By clicking buttons in the toolbar, a user can see spectral alignment of y ion tags, b ion tags, theoretical y-ion peaks and theoretical b-ion peaks respectively. Figure 2. MassPective screen shot. This is the interpretation of a spectrum corresponding to the peptide ‘GKGGKGLGKGGAKR’ of histone. It shows spectral alignments of y ion tags, theoretical y-ion peaks, and their ion annotation in red and those of their b counterparts in blue.