How does one specify if input data submitted to SAINTexpress are spectral counts or MS1 intensities? Also, should MS1 intensities be Log transformed?
Thank you
Welcome @Bernard
We can help with usage for tools available at a Galaxy server at this forum.
I can find these tools in our application repository but the versions are much older and are probably not the versions you are working with. Would you be able to clarify more?
We’ll need to know which server you are working at (URL, find this at the top of your browser window) and which exact tool (find this at the top of the tool form).
Then, for general help with this analysis domain, and alternative tools, we have some 
tutorials that may be of interest! The initial slides cover some of the data flow through tools.
With this tutorial specifically likely to help. You would be able to run through most of these tutorials at the UseGalaxy.eu public Galaxy server.
Hope this helps! 
Thank you so much for your answer!
Here is the URL: http://apostl.moffitt.org/
The tool that I am using is: SAINTexpress (Galaxy Version 1.0.0)
The stand-alone version of SAINTexpress can analyze either spectral counts or intensity data. Can you tell which of the two calculations the Galaxy implementation is performing and if there is a way to switch between them?
Thanks again,
Bernard
Hi @Bernard
Thanks for clarifying!
These tools are hosted on a special server, and details about the configuration/parameters would be better clarified by the people who wrote the tool suite, but maybe we can help here, too! On the server homepage, click into the Contact tab. The email addresses you can write to are listed out.
That said, from reviewing the tool form, it seems that you can provide either type of data in the input file.
Server → http://apostl.moffitt.org/
Tool → SAINTexpress (Galaxy Version 1.0.0)
Help content on the tool form clarifying the input format
SAINTexpress
This tool will read in a Bait File, Prey File, and Inter File and analyze them using the latest version of SAINTexpress.
1) Interactions File
Please specify an Inter file for SAINTexpress analysis. An Inter file should contain four columns: IP name, bait name, prey name, and spectral counts or intensity values, depending on the mode of quantification.
Then, to learn how to prepare those inputs, the server homepage has a link to the APOSTL Walkthrough here → GitHub - bornea/APOSTL: APOSTL is an interactive affinity proteomics analysis software developed to reformat affinity proteomics data (both spectral counting and MS1) for input into the SAINTexpress statistical package and to visualize the output(s).
This links to the Shared Data → Published Workflows view here → Galaxy | Published Workflows
These demonstrate the pathway through the tools. Each tool will have a link to the guides and related publications.
So, for your question here:
If you used an intensity‑based workflow, then the 4th column should reflect those intensity values. Link to one of the shared workflows on the server you can compare to for this kind of data.
Then, the other three generate spectral counts. Screenshot from the server:
If you click on any of those workflows, you’ll be able to review the tools and parameters used. If you generated the data yourself outside of the server, comparing will still probably help to determine what you have now plus how to format it (the guide had a lot of formatting advice!).
Hope this helps but please let us know if it actually does!