title: Identification of related peptides through the analysis of fragment ion mass shifts.
abstract: Mass spectrometry (MS) has become the method of choice to identify and quantify proteins, typically by fragmenting peptides and inferring protein identification by reference to sequence databases. Well-established programs have largely solved the problem of identifying peptides in complex mixtures. However, to prevent the search space from becoming prohibitively large, most search engines need a list of expected modifications. Therefore, unexpected modifications limit both the identification of proteins and peptide-based quantification. We developed mass spectrometry-peak shift analysis (MS-PSA) to rapidly identify related spectra in large data sets without reference to databases or specified modifications. Peptide identifications from established tools, such as MASCOT or SEQUEST, may be propagated onto MS-PSA results. Modification of a peptide alters the mass of the precursor ion and some of the fragmentation ions. MS-PSA identifies characteristic fragmentation masses from MS/MS spectra. Related spectra are identified by pattern matching of unchanged and mass-shifted fragment ions. We illustrate the use of MS-PSA with simple and complex mixtures with both high and low mass accuracy data sets. MS-PSA is not limited to the analysis of peptides but can be used for the identification of related groups of spectra in any set of fragmentation patterns.
authors: Institute of Food Research , Norwich Research Park, Norwich NR4 7UA, United Kingdom.
authors: Thomas
authors: T
authors: Wilhelm
authors: Alexandra M E
authors: AM
authors: Jones
mesh_terms: D030562:Databases, Protein; D007477:Ions / Q000032:analysis / Q000737:chemistry; D008970:Molecular Weight; D010446:Peptide Fragments / Q000032:analysis* / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D007477:Ions; D010446:Peptide Fragments