Peptide and PTM identifcation by MS/MS

CREATED: 200712310820 ** Background

• PTM - modification of amino acids
• DeNovo algorithms ** Lutefisk ** PepNovo ** Peaks
• Database algorithms ** Sequest ** Mascot
• Combined ** Inspect - generate tags using denovo methods, use tags in candidate selection of db search
• Spectrum graph ** consider all paths from source to dest ** which are the common suboaths? ** using multiple MS spectrum from different labs

** Approach

• coarse filtering (SoM)
• generate tags by denovo methods
• fine filtering ** by spectrum comparison/tags ** scoring peptide, share peaks count + length of matched tags ** scoring PTM

** Experiments

• Data sources ** Peptide Atlas ** OPD ** ISB
• Experiment ** quality of tags ** effect of search distance in MPRQ ** ratio of completely correct peptides ** efficiency ** simulated PTM