Identification of Related Peptides through the Analysis of Fragment Ion Mass Shifts

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.