TIMS²Rescore

Introduction

TIMS²Rescore is a specialized version of MS²Rescore for timsTOF DDA-PASEF data. This guide provides an overview of how to use TIMS²Rescore effectively.

Installing TIMS²Rescore

TIMS²Rescore is part of the ms2rescore package. Check out the Installation instructions to get started.

Usage

To use TIMS²Rescore, follow these steps:

  1. Prepare your input files:

    • To boost DDA-PASEF peptide identifications, TIMS²Rescore requires the spectrum files from the timsTOF instrument and the PSM files with identifications from a supported search engine.

    • Make sure that the PSM file format comes from a supported search engine or is a standard format such as mzIdentML (See supported file formats).

    • Spectrum files can directly be passed as .d or miniTDF raw data or can optionally be first converted to mzML or MGF. We recommend using the format that was passed to the search engine.

  2. Run tims2rescore:

    • Open a terminal or command prompt.

    • Navigate to the directory where your input files are located.

    • Execute the following command:

      tims2rescore -p <path_to_psm_file> -s <path_to_spectrum_file>

    Replace <path_to_psm_file>, <path_to_tims_file>, and <path_to_output_file> with the actual paths to your input and output files.

    note

    By default, specialized timsTOF models will be used for predictions. Optionally you can further configure TIMS²Rescore through a configuration file. For more information, refer to the Configuration tab in the user guide.

  3. Review the results:

    • Once the tims2rescore process completes, you will find the rescoring results in the same directory as the input files.

    • If you want a detailed report of the rescoring performance, you can either give the set write_report to True in the configuration file, use the –write_report option in the tims2rescore command line. Alternatively, run the following command after rescoring:

      ms2rescore-report <output_prefix>

      Replace <output_prefix> with the actual output prefix of the result files to the output file. For instance, if the output file is identifications.psms.tsv, then the output prefix is identifications.

Additional options

tims2rescore provides additional options to customize rescoring. You can explore these options by running the following command:

tims2rescore --help