Interconversion of Peptide Mass Spectral Libraries Derivatized with iTRAQ or TMT Labels.

Autor:	Zhang Z; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Yang X; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Mirokhin YA; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Tchekhovskoi DV; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Ji W; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Markey SP; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Roth J; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Neta P; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States., Hizal DB; Antibody Discovery and Protein Engineering Department, MedImmune LLC , One MedImmune Way, Gaithersburg, Maryland 20878, United States., Bowen MA; Antibody Discovery and Protein Engineering Department, MedImmune LLC , One MedImmune Way, Gaithersburg, Maryland 20878, United States., Stein SE; Mass Spectrometry Data Center, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
Jazyk:	angličtina
Zdroj:	Journal of proteome research [J Proteome Res] 2016 Sep 02; Vol. 15 (9), pp. 3180-7. Date of Electronic Publication: 2016 Aug 08.
DOI:	10.1021/acs.jproteome.6b00406
Abstrakt:	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.
Databáze:	MEDLINE
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