• Introduction to MS-Angel
• Installation and administration
• The graphical interface in 5 tabs
• User case example

The MS Angel software allows you to easily manage your acquisition files. It offers several levels of file processing, including:
- file conversions, from RAW and WIFF files;
- peaklists identifications using one or several search engines (Mascot fully supported, OMSSA is being integrated);
- import of identification results within Proline.

The design of workflows and tasks provides a high level of automation and control.

See the dedicated page.

• Workflow history: visualize tasks, giving details about the progression of the workflow on each file of the selected task.
• Identification history: visualize tasks including an MS identification step, giving details about the search engine, search parameters, and identification results for each file of the selected task.
• New task: design and launch a new task.
• Search parameters: create, import, visualize and modify search parameters templates.
• Log events: know about the last notable events in tasks execution [not yet implemented].

We will follow the example of a user willing to launch a task executing :
- the conversion of RAW acquisition files into peaklists,
- a peaklist identification using Mascot,
- the import of identification results into an existing Proline project.

For this, we will see how to go through each step: 1. Create a search parameters template 2. Design the task (input files, workflow…) 3. Visualize the task progression and results.

For some of these steps, several options will be suggested and explained.

Go to the “Search parameters” tab, then to the search engine-specific subtab.

There a several ways to create a template:

Option 1: Fill the form by hand

Fields whose names are marked by a star are mandatory.
Keywords can be used (within diples) for the fields 'User name' and 'Search title'. The list of available keywords and their meaning is displayed by clicking on the help icon.
Several databases can be selected by clicking on the databases names while pressing the shift key (or the Ctrl key to select a range of entries).
To add some PTMs to the 'Fixed modifications' list, select them in the complete list of modifications (on the right), then click on the top '<' button. To remove modifications from the 'Fixed modifications' list, select them within the 'Fixed modifications' list then use the top '>' button. This works the same way for 'Variable modifications', using the bottom '<' and '>' buttons.

Then save your new template by clicking 'Save parameters'. You must provide your template a name, and an owner within Proline users.