Contacts
Nuno Bandeira [bandeira (at) cs.ucsd.edu]Summary
It is well known in the proteomics community that the identification of post translational modifications (PTMs) is critical to understanding dynamic systems within the cell. In standard database search, adding different types of modifications and allowing more modifications per peptide cuts down on the sensitivity due to an increase in the search space. This makes the ability to search for PTMs without a priori knowledge essential, especially in samples which are highly modified or are likely to contain unexpected modifications.
Spectral networks (SpecNets) detect and identify groups from similar peptides with differing PTMs or sequence variants. Unlike other blind search methods which align spectra to a database, using pairs of spectra significantly reduces the search complexity by limiting to a single mass shift between spectra. Peptide identifications for a subset of spectra in a network are seeded from another source such as an unmodified database search, de novo or spectral libraries. Since modifications are not essential for these seed annotations, the search space is limited. Having the spectrum of a modified peptide paired with an unmodified peptide allows us to reconstruct probable PTM identifications based on the mass shifts between paired peaks.
The link below is an illustrates of a spectral network identified on a sample of cataractous lens:
