Analysis of reproducibility of proteome coverage and quantitation using isobaric mass tags (iTRAQ and TMT)

Tammy M. Casey, Javed M. Khan, Scott D. Bringans, Tomas Koudelka, Pari S. Takle, Rachael A. Downs, Andreja Livk, Robert A. Syme, Kar Chun Tan, Richard J. Lipscombe

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Abstract

This study aimed to compare the depth and reproducibility of total proteome and differentially expressed protein coverage in technical duplicates and triplicates using iTRAQ 4-plex, iTRAQ 8-plex, and TMT 6-plex reagents. The analysis was undertaken because comprehensive comparisons of isobaric mass tag reproducibility have not been widely reported in the literature. The highest number of proteins was identified with 4-plex, followed by 8-plex and then 6-plex reagents. Quantitative analyses revealed that more differentially expressed proteins were identified with 4-plex reagents than 8-plex reagents and 6-plex reagents. Replicate reproducibility was determined to be ≥69% for technical duplicates and ≥57% for technical triplicates. The results indicate that running an 8-plex or 6-plex experiment instead of a 4-plex experiment resulted in 26 or 39% fewer protein identifications, respectively. When 4-plex spectra were searched with three software tools - ProteinPilot, Mascot, and Proteome Discoverer - the highest number of protein identifications were obtained with Mascot. The analysis of negative controls demonstrated the importance of running experiments as replicates. Overall, this study demonstrates the advantages of using iTRAQ 4-plex reagents over iTRAQ 8-plex and TMT 6-plex reagents, provides estimates of technical duplicate and triplicate reproducibility, and emphasizes the value of running replicate samples. © 2016 American Chemical Society

Original languageEnglish
Pages (from-to)384-392
Number of pages9
JournalJournal of Proteome Research
Volume16
Issue number2
Early online date7 Dec 2016
DOIs
Publication statusPublished - 3 Feb 2017

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Casey, T. M., Khan, J. M., Bringans, S. D., Koudelka, T., Takle, P. S., Downs, R. A., ... Lipscombe, R. J. (2017). Analysis of reproducibility of proteome coverage and quantitation using isobaric mass tags (iTRAQ and TMT). Journal of Proteome Research, 16(2), 384-392. https://doi.org/10.1021/acs.jproteome.5b01154
Casey, Tammy M. ; Khan, Javed M. ; Bringans, Scott D. ; Koudelka, Tomas ; Takle, Pari S. ; Downs, Rachael A. ; Livk, Andreja ; Syme, Robert A. ; Tan, Kar Chun ; Lipscombe, Richard J. / Analysis of reproducibility of proteome coverage and quantitation using isobaric mass tags (iTRAQ and TMT). In: Journal of Proteome Research. 2017 ; Vol. 16, No. 2. pp. 384-392.
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Casey, TM, Khan, JM, Bringans, SD, Koudelka, T, Takle, PS, Downs, RA, Livk, A, Syme, RA, Tan, KC & Lipscombe, RJ 2017, 'Analysis of reproducibility of proteome coverage and quantitation using isobaric mass tags (iTRAQ and TMT)' Journal of Proteome Research, vol. 16, no. 2, pp. 384-392. https://doi.org/10.1021/acs.jproteome.5b01154

Analysis of reproducibility of proteome coverage and quantitation using isobaric mass tags (iTRAQ and TMT). / Casey, Tammy M.; Khan, Javed M.; Bringans, Scott D.; Koudelka, Tomas; Takle, Pari S.; Downs, Rachael A.; Livk, Andreja; Syme, Robert A.; Tan, Kar Chun; Lipscombe, Richard J.

In: Journal of Proteome Research, Vol. 16, No. 2, 03.02.2017, p. 384-392.

Research output: Contribution to journalArticle

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AU - Casey, Tammy M.

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AU - Lipscombe, Richard J.

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