The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics

We present a mass spectral library-based
method to identify tandem
mass spectra of peptides that contain unanticipated modifications
and amino acid variants. We describe this as a “hybrid”
method because it combines matching both ion m/z and mass losses. The mass loss is the difference between
the mass of an ion peak and the mass of its precursor. This difference,
termed DeltaMass, is used to shift the product ions in the library
spectrum that contain the modification, thereby allowing library product
ions that contain the unexpected modification to match the query spectrum.
Clustered unidentified spectra from the Clinical Proteomic Tumor Analysis
Consortium (CPTAC) and Chinese hamster ovary cells were used to evaluate
this method. The results demonstrate the ability of the hybrid method
to identify unanticipated modifications, insertions, and deletions,
which may include those due to an incomplete protein sequence database
or to search settings that exclude the correct identification, in
high-resolution tandem mass spectra without regard to their precursor
mass. This has been made possible by indexing of the m/z value of each fragment ion and its difference
in mass from its precursor ion.