Hi Ramon,

I think you'll find that both IsobariQ (http://folk.uio.no/magnusar/isobariq/index.html) and Rover (https://code.google.com/p/compomics-rover/) are freely available.

I have used IsobariQ in the past and it has served me well, most of the time. I had an issue with a new data set where it kept on picking the wrong reporter ion for one of the labels (I can't recall which now, but there was a nearby 'noise' peak). No matter what I did with the settings, I couldn't get it to select the correct ion all the time. Clearly this what not helpful, so I had to use another package. In this case I ended up using ProtienPilot (which is commercial, and expensive, from AB SCIEX).

I have also had a go with Rover, but I've had trouble loading the data into Rover and then performing the analysis. The main problem here has been a lack of time on my behalf to fully evaluate the package. Generally speaking the software out of this group is excellent and I still have Rover on my list of software to evaluate. So I would suggest you give it a try. One of the main attractions of this software is the ability to combine data from different quantitative programs.

Regards,

Peter

Thanks a lot Hans,

I've been using IsobariQ during last year too. I didn't have notice about pick picking problems. I have compared recently IsobariQ and Proteome Discoverer results, with the same raw data, and they were quite similar. Maybe it is a question about sample/ raw data. In our lab we perform a high threshold precursor intensity. So we expect a good ITRAQ labelling. On the other hand, this is a problem that we have to quantify very/low abundant proteins. I will check deeply my new data results.

Regards,