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

Published

July 7, 2016

Author(s)

Zheng Zhang, Xiaoyu Yang, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Weihua Ji, Sanford P. Markey, Pedatsur Neta, Bowen A. Michael, Stephen E. Stein

Abstract

Derivatizing peptides with isobaric tags such as iTRAQ and TMT is widely employed in proteomics due to their ability to multiplex quantitative measurements. We recently made publicly available a large peptide library derived from iTRAQ 4-plex labeled spectra. This resource cannot be 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 ‘cleaning’ 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. Overall this interconversion strategy provides a practical way to extend results from one derivatizing method to others that share related chemistry and do not significantly alter fragmentation profiles.

Citation

ACS Journal of Proteome Research

Volume

15

Issue

9

Pub Type

Journals

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DOI Link

Keywords

peptide mass spectral library, iTRAQ, TMT, isobaric tag, spectral conversion

Citation

Zhang, Z. , Yang, X. , Mirokhin, Y. , Tchekhovskoi, D. , Ji, W. , Markey, S. , Neta, P. , Michael, B. and Stein, S. (2016), Interconversion of Peptide Mass Spectral Libraries Derivatized with iTRAQ or TMT Labels, ACS Journal of Proteome Research, [online], https://doi.org/10.1021/acs.jproteome.6b00406 (Accessed October 21, 2025)