Note: This page will give you the steps of the most straigth-forward workflow in Proline. To see more details on what can be done and how, please consult the 'How To' page.

No matter which User Interface (Studio or Web) you will use, Proline's workflow remains the same:

1. If you plan to use the quantitation features of Proline, you'll need to register the Raw Files and their corresponding mzDB file into Proline's database in first place. This is an action you can perform aside from any project.
2. Once your files are ready to use, you must create a project. A project is attached to your user account, but you can “share it” with other users, so they can see it from their own account.
3. The first thing you need to do in your fresh new project is to import Result Files into it and associate them with the Raw Files you have registered, so that you will be able to create identification datasets you want to validate and quantitation experimental design based on your analyses.
4. Once your files are imported, you assemble them as datasets on which you will launch validation tasks with dedicated parameters
5. You can then launch a quantitation analysis by using your validated identification summaries, by re-creating you experimental, set up your own parameters and ratios.

The Raw Files and their corresponding mzDB files are stored on your servers but they must be “registered” and paired into Proline's database.

See how to do this in Proline Web. In Proline Studio actually only mzDB files are taken into account. You specify them during the quantitation process

A user can have many projects and share them with others. It's the place where you will import your Result Files (.dat, .omx), set up your validation and quantitation datasets

Read more about project creation in Proline Studio and Proline Web.

Once your project has been created, you'll need to import result files into it. This consists of storing your files data in Proline's databases. This is the first “task based” action will perform: Proline will run this action for a few minutes and you will be noticed when it's done.

See how to import files from the Proline Studio and the Proline Web interfaces.
Note that you can also import files from MS-Angel ( discover MS-Angel).

Once your files have been imported to your project's database, you can use them as dataset on which you will perform validation operations. Datasets can be assembled under “aggregates” or treated as-is (in Proline Studio only). Once you've created a dataset with one or more files, you can launch a validation task on it, and then browse its result in what's called an Identification Validation Summary.

How to create a Dataset: in Proline Studio / in Proline Web

Hot to validate a Dataset: in Proline Studio / in Proline Web

Quantitations are built around your Experimental Design. You are able to recreate your technical and biological replicas hierarchy in Proline, set up your extraction parameters, define the ratios of your analysis and then launch the task.

See how it's done in Proline Studio and Proline Web