title: Interconversion of Peptide Mass Spectral Libraries Derivatized with iTRAQ or TMT Labels.
abstract: Derivitization of peptides with isobaric tags such as iTRAQ and TMT is widely employed in proteomics due to their compatibility with multiplex quantitative measurements. We recently made publicly available a large peptide library derived from iTRAQ 4-plex labeled spectra. This resource has not been used for identifying peptides labeled with related tags with different masses, because values for virtually all masses of precursor and most product ions would differ for ions containing the different tags as well as containing different tag-specific peaks. We describe a method for interconverting spectra from iTRAQ 4-plex to TMT (6- and 10-plex) and to iTRAQ 8-plex. We interconvert spectra by appropriately mass shifting sequence ions and discarding derivative-specific peaks. After this "cleaning" of search spectra, we demonstrate that the converted libraries perform well in terms of peptide spectral matches. This is demonstrated by comparing results using sequence database searches as well as by comparing search effectiveness using original and converted libraries. At 1% FDR TMT labeled query spectra match 97% as many spectra against a converted iTRAQ library as compared to an original TMT library. Overall this interconversion strategy provides a practical way to extend results from one derivatization method to others that share related chemistry and do not significantly alter fragmentation profiles.
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Yang
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: Weihua
authors.initials: W
authors.lastname: Ji
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: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Jeri
authors.initials: J
authors.lastname: Roth
authors.affiliation: Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
authors.forename: Pedatsur
authors.initials: P
authors.lastname: Neta
authors.affiliation: Antibody Discovery and Protein Engineering Department, MedImmune LLC , One MedImmune Way, Gaithersburg, Maryland 20878, United States.
authors.forename: Deniz Baycin
authors.initials: DB
authors.lastname: Hizal
authors.affiliation: Antibody Discovery and Protein Engineering Department, MedImmune LLC , One MedImmune Way, Gaithersburg, Maryland 20878, United States.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Bowen
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: D030562:Databases, Protein; D013058:Mass Spectrometry; D008970:Molecular Weight; D019151:Peptide Library; D040901:Proteomics / Q000379:methods*; D013194:Staining and Labeling
chemical_list: D019151:Peptide Library
keywords: TMT; iTRAQ; isobaric tag; peptide mass spectral library; spectral conversion