Graphical user interface
Installation
The MS²Rescore desktop application can be installed on Windows with a one-click installer. Alternatively, or on other platforms, follow the Python package installation instructions.
Starting the application
If installed with the one-click installer, simply start MS²Rescore from the start menu or with the
desktop shortcut. Otherwise, start the application from the
command line with the command ms2rescore-gui or with
python -m ms2rescore.gui.
Application overview
The MS²Rescore graphical user interface is divided into three main sections:
A side bar with references, window controls, and the current version number.
The configuration pane with input file selection, and parameter configuration.
The application log pane with the status output.
On the bottom of the window, the application log level can be selected. The log level determines which messages are shown in the application log pane. On the bottom right, the application can be started with the “Start” button. The “Stop” button can be used to stop the application at any time during the execution.
Overview of the MS²Rescore desktop application.
Configuring MS²Rescore
Input file selection
The main input for MS²Rescore are the PSM file(s) (search engine output) and the spectrum file(s). See Input files for more information.
One or more PSM files can be selected from the file system with the “Browse files” button under. To make ensure correct reading of the file, specify the file type with from the drop-down menu.
PSM file selection
PSM file type selection
To select a single spectrum file (mzML or MGF), click the “Browse files” button. To select a folder with spectrum files, click the “Browse directories” button.
Spectrum file selection
Optionally, for protein inference information, a FASTA file can also be provided. Ensure that this file contains the same protein sequences as the search database used for the search engine. If a FASTA file is provided, protein digestion settings may need to be configured in the rescoring engine configuration.
Number of processes
The number of processes can be configured to run the application in parallel. The default is to use all available CPU cores. The number of processes can be reduced to avoid overloading the system or to avoid memory issues. A number under 16 is recommended.
Modification mapping
Depending on the search engine, the peptide modification labels will have to be mapped
to labels that can be understood by MS²Rescore. For example, X!Tandem uses mass shift labels, such
as +57.02146 for carbamidomethylation. However, tools such as DeepLC requires the atomic
composition for all modifications. As this cannot be derived from the mass shift (or other labels
that are not known to MS²Rescore), a mapping has to be provided.
Modification mapping configuration. Click the plus sign to add more rows.
In modification mapping, click the plus sign to add more rows to the table, or click the minus sign to remove rows. In the first column “Search engine label”, enter the modification label as it appears in the PSM file. In the second column “ProForma label”, enter a ProForma-compatible modification label. More information on accepted labels can be found in Parsing modification labels.
Modification mapping configuration for the X!Tandem example. Mass shift labels from X!Tandem are mapped to ProForma UniMod labels.
Fixed modifications
If the search engine PSM file does not contain information on which fixed modifications were used,
this must be specified in the MS²Rescore configuration. At the time of writing, only MaxQuant
msms.txt` files do not contain this information. For all other search engines, this information
is contained in the PSM file and the following field can be left empty.
Advanced options
Most advanced options are only required for specific use cases or with specific search engine PSM files. All options are listed in the Configuration section of the user guide.
In the X!Tandem example, only the PSM ID regex pattern option is required. This option is used to extract the spectrum ID from the PSM file. The spectrum ID is used to match the PSM to the spectrum file. See Mapping PSMs to spectra for more information.
Advanced options
For reference, all parameters for the X!Tandem example are also listed in the example configuration file on GitHub.
Starting the rescoring process
After the configuration is complete, click the “Start” button to start the rescoring process. The application will show the progress in the application log pane. The log level can be changed before the run to show more or less information.
Running application with log output
A pop up will appear when the application is finished, or when an error occurred. If an error has occurred, the error message in the pop up should provide some insight into what went wrong. If the error message is not clear, please report the issue on the GitHub issue tracker or post your question on the Discussion forum.
Pop up when MS²Rescore is finished
Viewing the results
After a successful run, the output files can be found in the directory of the input PSM file, or
in the specified output directory. The most important files are the *.ms2rescore.psms.tsv file,
which contains all PSMs with their new scores, and the *.ms2rescore.report.html file, which
contains interactive charts that visualize the results and various quality control metrics. See
Output files for more information.
Overview of the output files after rescoring the X!Tandem example.
Double click the *.ms2rescore.report.html file to open it in the default web browser:
Rescoring QC report with interactive charts.