title: The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics.
abstract: 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.
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Meghan C
authors.identifier: 0000-0001-7231-0655
authors.initials: MC
authors.lastname: Burke
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Yuri A
authors.initials: YA
authors.lastname: Mirokhin
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Dmitrii V
authors.initials: DV
authors.lastname: Tchekhovskoi
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Sanford P
authors.initials: SP
authors.lastname: Markey
authors.affiliation: Analytical Sciences, MedImmune LLC , One MedImmune Way, Gaithersburg, Maryland 20878, United States.
authors.forename: Jenny
authors.initials: J
authors.lastname: Heidbrink Thompson
authors.affiliation: Analytical Sciences, MedImmune LLC , One MedImmune Way, Gaithersburg, Maryland 20878, United States.
authors.forename: Christopher
authors.initials: C
authors.lastname: Larkin
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Stein
mesh_terms: D000465:Algorithms; D000818:Animals; D016466:CHO Cells; D045744:Cell Line, Tumor; D003412:Cricetulus; D016208:Databases, Factual; D030562:Databases, Protein; D006801:Humans; D007477:Ions; D008970:Molecular Weight; D040901:Proteomics / Q000379:methods* / Q000592:standards; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D007477:Ions
keywords: peptide mass spectral library; post-translational modifications; spectral library searching