General Information

ProteoSAFe is a web server for analyzing your MS/MS proteomics data online. The Center for Computational Mass Spectrometry has many tools, and ProteoSAFe allows you to use all of them within the framework of a single user interface. The server utilizes a distributed computational cluster, so your analysis should finish fairly quickly. Please contact us with any questions you may have.

Using the Server

The interface should be fairly self-explanatory. Just choose the workflow (see below) and fill in the associated options. Then upload your data files, assign them to the proper file categories of your search, and click "Submit". After the analysis is completed, you can browse or download the results.

In addition, much of the interface comes with tool-tips. If you hover your mouse over a piece of text and see a question mark next to the mouse pointer, then context-sensitive help exists. A floating help bubble should appear, which you can "pin" in place by simply clicking on the original page text. Then click on the small "X" in the upper right corner of the help bubble to remove it.

Current Workflows

For a more in-depth discussion of the various tools offered as ProteoSAFe workflows, please visit our software development page here.


How do I know what to choose for parameter values?
We have set up the interface with default parameters that should work well. For questions about a specific parameter, read the tool-tip.

How do I view the results of my search?
If you sign up for an account, then all searches are kept for you. You can view the results at any time by clicking on Jobs in the main navigation bar. You will see a list of all your jobs. If you don't have an account, then then you can bookmark the submittion page for your job, which is a static link (deleted after 1 month).

How do I know when my job is finished?
If you sign up for an account, then you will receive an email when you search completes.