# The program's graphical user interface

Proteomics data exploration, with &xtpcpp;, entails, for a large part, the following steps:

- Configuration of the &xtandem; external software that runs the database searches (producing peptide vs mass spectrum matches, leading to the peptide identifications);

- Loading of the database files (both the organism-specific databases and optional contaminants databases);

- Loading of the mass spectrometry data acquisition files;

- Running of &xtandem; from inside of &xtpcpp;, with production of a set of peptide vs mass spectrum matches (peptide identification results);

- Load the data produced during the previous step;

  &xtpcpp; can also handle peptide vs spectrum matches data (peptide identification data) from other software with the following formats:

  - mzIdentML;

  - pepXML;

  - FIXME: quels autres ? Soyons exhaustifs.

- Relentless scrutiny of the peptide identification results. Optional modification of the results;

- Protein inference, that is, protein identification on the basis of the peptide identifications. &xtpcpp; has a powerful interface to ease the scrutiny of the protein groups (grouping) that leads ultimately to protein identification. The default protein groups calculated by &xtpcpp; can be modified by the user.

In this chapter, the graphical user interface is described in detail, going from the first step above to the last one.

## Starting a new &xtpcpp; working session

To start a session, run &xtpcpp; and the main program windows shows up as described in fig_xtpcpp-main-program-window.

### Main program window

The main program window contains three buttons described in detail in the text.

The main program window contains three buttons that start the following functions:

- Run X!Tandem identifications. See chap_running-xtandem-identifications.

- Load identification results (mzIdentML, pepXML, X!Tandem). See chap_loading-identification-results.

- Load an X!TandemPipeline project. See chap_loading-xtandempipeline-project.

## The Window Layout

The graphical interface of comprises a number of windows where data and informations are displayed. When first started, the program shows the main program window. Upon loading of a MS run data set from file, new windows do show up as described below (see fig_minexpert-whole-window-set):

- mineXpert2 main program window: this is an unintrusive window sporting the main menu;

- The Task monitors window, that displays all the ongoing tasks, always providing the user the ability to cancel an ongoing task;

- The Open MS run data sets window, that lists all the mass spectrometry data sets that have been loaded from file;

- The TIC/XIC chromatograms window

  TIC stands for total ion current and XIC stands for extracted ion current.

  where the various TIC/XIC chromatograms are displayed for the various mass spectrometry data files that have been loaded. There is, by definition, a single TIC chromatogram for each MS run data set currently loaded in the program. However, this window will also display ion current chromatograms that are computed as a result of an integration step from the other windows, like from the Mass spectra window or from the Drift spectra window. In this case, the chromatogram is an extracted ion current chromatogram (XIC chromatogram);

- The Mass spectra window, where the various mass spectra are displayed. A given mass spectrum may originate from a TIC chromatogram, from the MS run data set tableview window, from a drift spectrum, or even from a color map;

- The Drift spectra window, where the various drift spectra are displayed. Like stated before, drift spectra can originate from a variety of places;

- The TIC/XIC chrom. /Mass spec. color maps window, that contains int = f(rt, &mz;) color maps, two-dimensional representations of the relation between the retention time and the mass spectral data. The intensities are represented as colors in a gradient map;

- The Drift spec. /Mass spec. color maps window, that contains int = f(dt, &mz;) color maps, two-dimensional representations of the relation between the drift time and the mass spectral data (in ion mobility mass spectrometry experiments only). The intensities are represented as colors in a gradient map;

- The Console window, where the various messages or analysis data elements are displayed for the user to select, copy and paste in an electronic lab-book;

### General View of the Graphical User Interface

The position and size of all the windows can be stored for a later session

## The Main Program Window Menu

The menu bar in the main program window displays a number of menu items, reviewed below:

- File

  - File Open mass spectrum file(s) fully in memory : Select the mass spectrum file(s) to load. The mass spectral data read from disk are stored in memory. This means that if the file is greater than the available system memory (RAM), the user is urged to select the next menu;

  - File Open mass spectrum file(s) in streamed mode : Select the mass spectrum file(s) to load. The mass spectral data are read from disk, the TIC chromatogram and the MS run data set statistics are computed and then the data are freed. This file opening mode is compulsory when the mass data file is larger than the available system memory (RAM);

  - File Load mass spectrum from clipboard : Create a mass spectrum from a textual representation of &mzi; pairs in the same format as described above for the txt,asc file format;

  - File Analysis preferences : Set the preferences for the exploration results storage;

- Windows

  The menus are self-explanatory, as they explicitely explain which window is to be shown. The Save workspace menu records on disk the position and size of all the windows, so that upon reopening the program, the windows all position themselves at the recorded position and size;

- Utilities

  - Utilities XIC chromatogram extractions : Open a dialog window to set up XIC extractions for any one of the currently loaded mass spectral data set;

  - Utilities Isotopic cluster calculations : Open the window in which the isotopic cluster calculations are configured and run;

  - Utilities Mass peak shape calculations : Open the window in which the mass peak shape calculations can be configured and run.

- Help

  This menu's items show help about the program itself and also about the Qt libraries that were used to build it. These informations are essential in case the user wants to make a bug report.