# Import Mascot quantifications

This operation allows you to import Mascot emPAI quantifications from a set of Mascot CSV report files.

Usage

You can execute this operation by clicking the menu option Import/Import Mascot quantifications.

A dialog will appear allowing you to choose the directory containing the CSV files and other parameters to perform data normalization. As you can see in the following image, this dialog requires you to provide the following information:

- Quantifications CSV directory: the directory containing the CSV files generated by the Mascot quantification report. Please, note that you must select a directory and not the individual files. See the next section to know how to obain and organize these CSV files.
- Normalization level: the level at which normalization should be applied. You can choose one of the following:
  - Replicate: to perform the normalization by replicate.
  - Sample: to perform the normalization by sample.
  - Global: to perform the normalization taking into account all samples.
  - No normalization: if you don't want to calculate the normalized quantification values.
- Normalization factor: the normalization factor to use. You can shoose one of the following: Sum, to divide each value by the sum of all values at the specified normalization level; or Median, to divide each value by the median of all values at the specified normalization level.
- Condition comparison: the protein value to use to perform the statistical tests between conditions. You can choose one of the following: Normalized quantification, to perform the statistical tests using the normalized quantification values; or Protein mass, to perform the statistical tests using the protein mass value.

Import Mascot quantifications dialog

After clicking the Ok button, the imported Mascot quantifications are added as a Mascot quantifications datatype to the clipboard and automatically opened in the Mascot quantifications viewer.

Obtaining and organizing the Mascot CSV report files

The Mascot CSV report files can be obtained through the Mascot Search Results web interface as the following image shows.

Mascot Search Results web interface

After selecting the Export as CSV option, the following screen will appear, allowing you to select the information that you want to include in the reports. Here, you must select emPAI in the Protein Hit Information section in order to include the emPAI protein quantification values. To obtain the CSV files, click the Export search results button.

Mascot Export as CSV web interface

(click in the image to enlarge)

This way, you will obtain one CSV for each replicate in the dataset. In order to import these CSV files into S2P, you must rearrange them in the following way:

- Create one directory for each condition in the dataset.
- Place the CSV files in their corresponding condition directory.
- Make sure that each CSV file follows the following naming convention: sample_name.replicate_number.csv. This way, S2P will be able to know what are the samples in the dataset.
- Optionally, create a file named protein-masses.txt in each condition directory to indicate the amount of protein mass for each sample.

The example below shows a protein-masses.txt where the protein masses for samples Sample_1 and Sample_2 are defined:

    		Sample_1=100
    		Sample_2=200

For instance, if you have two conditions (Condition_A and Condition_B) in your dataset and two samples with three replicates for each condition, this is how your Quantifications CSV directory may look like:

    		.
    		|-- Condition_A
    		|   |-- protein-masses.txt
    		|   |-- Sample_A1.1.csv
    		|   |-- Sample_A1.2.csv
    		|   |-- Sample_A1.3.csv
    		|   |-- Sample_A2.1.csv
    		|   |-- Sample_A2.2.csv
    		|   |-- Sample_A2.3.csv
    		|
    		|-- Condition_B
    		    |-- protein-masses.txt
    		    |-- Sample_B1.1.csv
    		    |-- Sample_B1.2.csv
    		    |-- Sample_B1.3.csv
    		    |-- Sample_B2.1.csv
    		    |-- Sample_B2.2.csv
    		    |-- Sample_B2.3.csv