The purpose of the Data Analyzer is to easily do calculations/comparisons on data.

To open the data analyzer, you have two possibilities:

- you can use the dedicated button that you can find in the toolbar of all views. If you use this button, the corresponding data is directly sent to the data analyzer.

- you can use the menu “Window>Data Analyzer”

In the Data Analyzer view, you can access to all data views, to some functions and graphics. In the following example, we create a graph by adding by Drag & Drop the Spectral Count Data and the BBinomial function. Then we link them together.

You have to specify the parameters of the BBinomial Function : right click on the function and select the “settings” menu

In the settings menu, select the two groups of columns on which you want to perform the BBinomial function. When the parameters are set, the calculation is started immediately and an hourglass icon is shown.

When the calculation is finished : the hourglass icon becomes a green tick, and the user can right click and select the “Display” menu to see the result.

This function is used by ProStar Macro to compute the FDR.

More information: http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf

Join data of two tables according to selected key.

Perform a difference between two joined table data according to a selected key. When a key value is not found in one of the data source table, the line is displayed as empty. For numerical values a difference is done and for string values, the '<>' symbol is displayed when values are different.

Calibration Plot for Proteomics is discribed here : https://cran.r-project.org/web/packages/cp4p/index.html

bbinomial function is useful for Spectral Count Quantitations

This function is used by ProStar Macro. Two tests are available : Welch t-test and Limma t-test.

More information: http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf

filter function let the user filter some rows of a matrix according to settings on columns

This module lets you import data from a CSV or TSV file. Then you can do calculations and display these data directly in Proline Studio.

This function is used by ProStar Macro to remove rows with too many missing quantitative values.

The available missing values algorithm are:

• Whole Groups: The lines (across all groups) in the quantitative dataset which contain less non-missing value than a user-defined threshold are deleted.
• For every group: The lines for which each condition contain less non-missing value than a user-defined threshold are deleted.
• At least one group: The lines for which at least one condition contain less non-missing value than a user-defined threshold are deleted.

This function is used by ProStar Macro to imput missing values.

More information: http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf

This function is used by ProStar Macro to normalize quantitative values.

More information on algorithms : http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf

pvalue and ttd functions are useful for XIC Quantitations

1 : Add XIC Data to Data Analyzer from the Protein Set View.

2 : Add Prostar Macro by a drag and drop and link XIC Data to the Macro

3 : Process the Graph by clicking on the button

During the process, the Data Analyzer will ask you settings for each function.

4 : Filter is needed only if you want to remove contaminants. Settings can be validated with no parameters if you don't need it.

5 : Log is needed to log abundances (Data from Proline). For Data coming from Max Quant, data is already logged.

6 to 12 : follow the settings asked ( you can find some help in Prostar documentation, or information in corresponding functions.)

During the process, results will be automatically displayed : calibration, scatter plot and FDR Result. If you want to look at other results, right click on a function and select “Display in New Window”

Prostar User Manual : http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf

Prostar Tutorial : http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_Tutorial.pdf