I'm thinking of doing some GeneOntology on some supplementary information I found in a paper (DOI: 10.1021/acs.jproteome.5b00770). However the information on identified proteins is available from both iTRAQ and iBAQ analysis. I'm not sure what the difference is or what one to use. What is the difference between the two?
Thank you.
Here is a nice 15-minute lecture that explains the techniques.
https://www.coursera.org/learn/experimental-methods/lecture/n7Z1J/lecture-3-quantification-in-proteomics
Use iTRAQ if money (expensive, yet robust!) is not limiting and for more accurate results.
Do not try iBAQ if in house proteomics expertise does not exist and resources are not limiting!
Results would differ both qualitatively and quantitatively from the two different methods as they operate on completely different principles of detection and quantification. To me, those results may not be comparable in terms of particular proteins, GO-wise: may be comparable!
Biswa
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