 The database-searching approach is convenient; however, in cases wherein the corresponding sequences are not included in the databases, the exact identification is difficult. It is necessary to turn to MS BLAST searching. Like the Sequence Tag search, this requires partial sequence information to be obtained from MS/MS data. Programs are available to generate candidate amino acid sequences from mass spectra, so-called de novo sequencing, but often time-consuming manual interpretation of spectra is necessary. In de novo sequencing, mass spectrometers have the advantage when it comes to generating sequence data for peptides in low femtomole quantities. MS/MS enjoys sensitivity, and speed, and does not require an external standard for each amino acid or amino acid variant. Another advantage is that MS/MS sequencing is never stopped by a blocked amino terminus, as is the case for Edman degradation.
We offer a de novo sequencing service labeled with 4-sulfophenyl isothiocyanate (SPITC), which facilitates the easy interpretation by the introduction of N-terminal sulfonated derivatives, in which software-generated peptide sequences are verified by manual inspection of the MS/MS spectra.
Bioinformatics. 2007 23(9):1068-1072
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