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
Pub Type: Journals
peptide mass spectral library, iTRAQ, TMT, isobaric tag, spectral conversion