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MODi: A Powerful and Convenient Web Server for Identifying Multiple Post-Translational Peptide Modifications From Tandem Mass Spectra

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MODi: A Powerful and Convenient Web Server for Identifying Multiple Post-Translational Peptide Modifications From Tandem Mass Spectra

Sangtae Kim et al. Nucleic Acids Res.

Abstract

MOD(i) (http://modi.uos.ac.kr/modi/) is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MOD(i), one can consider for analysis both the entire PTM list published on the unimod webpage (http://www.unimod.org) and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MOD(i) is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MOD(i)'s output in a user-friendly manner and helps users understand MOD(i)'s output quickly. In addition, one can perform manual de novo sequencing using MassPective.

Figures

Figure 1
Figure 1
A tag chain ‘__GG_glg_gga__’ for a spectrum from histone. A sequence of capital letters represents a forward tag, a sequence of small letters a reverse tag and each underline a gap. This tag chain consists of one forward tag ‘GG’, two reverse tags ‘glg’ and ‘gga’ and four gaps in between. A mass offset for a gap can be calculated by subtracting the mass of a gap from the size of its aligned segment of the spectrum. For example, the mass offset of the leftmost gap can be calculated as 41.947 Da, based on the size of aligned segment of 227.063(228.063 − 1) and the mass of the sequence ‘GK’ corresponding to the gap of 185.116 (Glycine: 57.021, Lysine: 128.095).
Figure 2
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.
Figure 3
Figure 3
A protein summary report generated by MassPective. It is a summary of the output of MODi for each identified protein, containing protein information and sequence coverage for proteins which correspond to input spectra. Also, for each interpreted spectrum, it gives a submitted mass, matched peptide sites in protein sequence, match score, a spectrum identifier and identified PTMs.
Figure 4
Figure 4
Manual sequencing by MassPective. If a user designates an area in the spectrum, a window pops up showing all possible combinations of one amino acid mass possibly with one PTM whose mass agrees with the difference of two peaks in the area with higher intensity than the intensity value of the designated line.
Figure 5
Figure 5
Interpretation for a spectrum with precursor ion 719.663 (2+) corresponding to a peptide ‘GKGGKGLGKGGAKR’ of histone. MODi first finds a tag chain __GG _glg_gga__, computes mass offsets of the gaps, which are 41.95, 41.92, 41.94 and 41.93 Da, respectively (shown in Figure 1). Every Lysine is interpreted with an acetylation and the estimation is evaluated by a scoring scheme.
Figure 6
Figure 6
Shows that MODi can find multiple PTMs in a single gap. It identifies a deamidation on ‘N’ and a di-methylation on ‘K’ in a gap ‘NGK’.

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