Getting started:
1. Create a new user profile in the menu "Profiles".
2. Select your profile name in the list of profiles and click on the "Open a session" button.
3. Click on "Configure a profile" in the menu "Profiles" and configure your profile by setting filters based on Mascot criteria.
4. Extract and validate your Mascot results with the "Mascot File Parser" module.
Menu description:
"Mascot File Parser": "Create and validate an experiment" to parse Mascot .dat files. "Open an experiment" to visualize your Mascot results filtered using your criteria previously defined in the menu "Configure a profile". "Generate a protein list" to edit a list of all previously validated proteins in your experiment. "Open a list" to access to a protein list already generated.
"Quantification": Before using this menu you have to run an external module called Extract Daemon to retrieve the intensity of previously validated peptides in MS Survey data."Process a quantification analysis" to perform the quantitative computation of the selected experiment. "Open an analysis" to access to an experiment already analyzed and quantified. "Create a quantification report" to generate a detailed report containing the quantification ratios of each protein in the experiment. "Open a quantififcation report" to visualize a report.
"Differential Analysis":"Open a list" to visualize the lists of validated proteins created in the MFP menu. "Compare two lists" to compare the lists of proteins from two experiments A and B and to generate three new lists: - one containing the specific proteins from experiment A, - one containing the specific proteins from experiment B, - one containing shared proteins from experiments A and B. "Merge two lists"(not yet implemented).
MFPaQ offers an export option to report software results in Microsoft Excel format ®.