protein identification

Reference: Bioinformatics, a pratical guide to the analysis of genes and proteins. Edited by Andreas D.Baxe

Different combinations of amino acids can add up to the same peptide mass, any single peptide mass can be produced by many proteins. While Peptide spectum, entire set of constituent peptide masses observed, is typically unique to a specific protein.

1.Peptide mass fingerprinting (PMF)


Programs: Mascot, PeptIdent, Profound, Genome Fingerprint Scanning.

2. Tandem MS
It contains a second stage of ms analysis in which selected peptides are broken down into even smaller pieces by collision-induced dissociation (CID: high-speed particles collide and cause peptide bonds to break). It results a set of charged peptides with one or more amino acids removed from either C- or N- terminus of the selected peptide. two method to analyze the Tamdem MS spectrum.
a. de novo approach
  Mass spectrum data -----------Amino acid sequence------------BLAST search
in this method, each peak in the ms/ms spectrum is assumed to be all possible ion type.
Problems:  PTMs, weak signal

b. uninterpreted ms/ms spectral matching
Use databases to produce hypothetical spectral, then compare with the observed experimental spectra and give a score indicating  how likely it is that the spectrum was produced by each possible peptide in the database.  Program: Sequest
Problems: computational intensive