Best itraq quantification method using Fusion

[Lifu Sheng]

Hi all,

I am just writing to what might be the best or most popular method to quantify ITRAQ data generated by Fusion Orbitrp.

Thank you.

Best,

Lifu

[Phillip Wilmarth]

Hi Lifu,

Is this 4-plex iTRAQ, or 8-plex, or TMT? How did you acquire the data on the Fusion? It supports several different acquisition modes. I have a Comet-based pipeline that does isobaric labeling:

https://github.com/pwilmart/PAW_pipeline

I only does TMT tags currently. Adding support for iTRAQ might be easy to do, if you are interested in using it. If you want to see how you can analyze quantitative data with notebooks and R, I have lots of examples here:

https://github.com/pwilmart/TMT_analysis_examples

Cheers,

Phil W.