PROTEOMIC PAIRWISE COMPARER TUTORIAL
Welcome to the Proteomic Pairwise Comparer tutorial. This module
is designed for use with PatternLab for proteomics,
requiring files in the .plp
format as input. Follow the steps below to effectively utilize the tool for
your proteomic analysis.
GETTING STARTED
1. Installation and Launch
1.1.
Download
the latest version of Proteomic Pairwise Comparer from the provided link.
1.2. Install the software on your computer.
1.3. Open Proteomic Pairwise Comparer to
begin.
2. File Selection
2.1. Click on "Choose plp file" and navigate to the desired .plp file on your computer.
3. File Classification
3.1. Assign a class to your file by using the
"Label the file's class option." This step is crucial for comparative
analysis.
Example:
|
Class |
Name |
Side |
|
1 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\08\08.sepr2 |
Left Side Driver 1 |
|
3 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\10\10.sepr2 |
Left Side Driver 2 |
|
5 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\16\16.sepr2 |
Left Side Driver 3 |
|
7 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\18\18.sepr2 |
Left Side Driver 4 |
|
9 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\20\20.sepr2 |
Left Side Driver 5 |
|
11 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\22\22.sepr2 |
Left Side Driver 6 |
|
13 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\24\24.sepr2 |
Left Side Driver 7 |
|
15 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\30\30.sepr2 |
Left Side Driver 8 |
|
17 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\32\32.sepr2 |
Left Side Driver 9 |
|
19 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\L\34\34.sepr2 |
Left Side Driver 10 |
|
2 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\07\07.sepr2 |
Right Side Driver 1 |
|
4 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\09\09.sepr2 |
Right Side Driver 2 |
|
6 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\15\15.sepr2 |
Right Side Driver 3 |
|
8 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\17\17.sepr2 |
Right Side Driver 4 |
|
10 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\19\19.sepr2 |
Right Side Driver 5 |
|
12 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\21\21.sepr2 |
Right Side Driver 6 |
|
14 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\23\23.sepr2 |
Right Side Driver 7 |
|
16 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\29\29.sepr2 |
Right Side Driver 8 |
|
18 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\31\31.sepr2 |
Right Side Driver 9 |
|
20 |
D:\Amanda\OneDrive\Doutorado\Doutorado\Vichy\Vichy\searched\R\33\33.sepr2 |
Right Side Driver 10 |
4. Setting Parameters
4.1. Specify the minimum number of samples
required for your analysis under the relevant option.
5. Analysis
5.1. Initiate the analysis by clicking on
"Calculate folds." This process will compare the protein expression
levels between your samples.
6. Visualization
6.1. The data can be visualized in a table
format for a comprehensive overview.
6.2. Selecting a protein in the table will
display a radar plot, which shows the fold change in each condition. Blue lines
indicate proteins that are upregulated, whereas red lines denote downregulated proteins.
