Identifying PTM

CREATED: 200701030652 Author: Pavel Pevzner

** Three Ideas

• Aho-Corasick algorithm
• Filtration, i.e. FASTA/BLAST
• Sequence alignment

** De Novo vs Database Search (paradox)

extract tags

** PepNovoTag ** covering set of tags (10 tags)

filter database

set of tags enable use of Aho-Corasick algorithm

** Post translational modification

• ~ 7200 types of PTM ** increases size of protein alphabet
• restrictive search ** fix types of modifications
• blind search
• similar peptide have dissimilar spectra
• convert spectra to sequence of 0 and 1 ** modifications -> insertion/deletion of blocks of zeros
• verifications ** look at which kinds of PTM occur on which amino acid, compare with knowm chemistry