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Input files
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PSM file(s)
===========

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``.


Spectrum file(s)
================

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.