Thursday, November 9, 2017

GiaPronto -- One-click quantification visualizations!

I don't know if I've ever sat down and mastered such a powerful data analysis tool in 4 times the time it took to get beautiful plots out of GiaPronto.  I seriously almost didn't write anything on the blog about it, because I was afraid more people using it would mean it wouldn't run so lightning quick for me.

I've been impressed with the ingenuity of GIA before. But now I have all these tools in a ridiculously easy web-interface?

Welcome to GiaPronto!

You pull your quantitative protein list you want to analyze (it only supports pairwise comparisons, but it's so fast, just do a bunch of them!) put them in the format it wants (I just exported my PD 2.2 result reports as Excel and deleted anything I didn't need, save it as a tab delimited .txt file input it into the interface and hit the Go button.  If you're using MaxQuant it's even easier. You don't have to change the titles of your Rows (columns?) to say iBAQ. They might already include this program-critical term!

It normalizes your data (as shown above) it makes PCA and volcano plots for you, it pulls out your list of significantly differential proteins which you can just export as full tables and ---

it does really powerful and intuitive biomarker analysis! "Hey, what proteins are my important biomarkers?" Don't change anything. Just hit the Go button and tab over!

It also does GO (Gene Ontology), but I don't have my data formatted correctly for that I think. AND I haven't even tried the PTM analysis functionality.

You can read more about it in this new paper at MCP here.


  1. Dear Ben,
    thank you very much for your very nice post. We hope the users will find GiaPronto helpful and simple to use, as we intended. We definitely welcome suggestions!


    1. Thanks for the great software! I'm going to be using it and I'll happily send you suggestions!

  2. Too bad the link ( isn't working since day one. It sounds like an interesting tool though.

  3. Tim,
    You might want to check your browser. Maybe it doesn't support it, or the website is blocked? I've used it several times since posting this -- and I can get on it this morning and load data just a few hours after you posted this comment.

  4. It seems our institution is blocking the website, i also tried different browsers and different PCs but all internally! That would explain it.
    Thank you for the clarification!