The peptide-spectrum match (PSM) file is generally the output from a proteomics search engine. This file serves as the main input to MS²Rescore.
The PSM file should contain all putative identifications made by the search engine, including both target and decoy PSMs. Ensure that the search engine was configured to include decoy entries in the search database and was operated with target-decoy competition enabled (i.e., considering both target and decoy sequences simultaneously during the search).
Attention!
As a general rule, MS²Rescore always needs access to all target and decoy PSMs, without any FDR-filtering. For some search engines, this means that the FDR-filter should be disabled or set to 100%.
One or multiple PSM files can be provided at once. Note that merging PSMs from different MS runs could have an impact on the correctness of the FDR control. Combining multiple PSM files should generally only be done for LC-fractionated mass spectrometry runs.
Various PSM file types are supported. The type can be specified with the psm_file_type option.
Check the list of :py:mod:`psm_utils` tags in the
:external+psm_utils:ref:`supported file formats <supported file formats>` section. Depending on the
file extension, the file type can also be inferred from the file name. In that case,
psm_file_type option can be set to infer.
Note
If a previous MS²Rescore run crashed during feature generation or rescoring, an intermediate
file (<prefix>.intermediate.psms.tsv) is automatically saved. This file contains all PSMs
with features that were successfully added up to that point. You can resume processing by
providing this file as the PSM file (-p <prefix>.intermediate.psms.tsv -t tsv) to skip
already completed feature generation steps.
Spectrum files are required for some feature generators. Both mzML and mgf formats are
supported. The spectrum_path option can be either a single file or a folder. If the
spectrum_path is a folder, MS²Rescore will search for spectrum files in the directory according
to the run names in the PSM file.