#####################
Modules documentation
#####################

.. toctree::
   :maxdepth: 2
   :glob:

   *

Links to active modules
=======================


- `Label-free quantification of precursor ions with DDA (QExactive) <https://proteobench.cubimed.rub.de/Quant_LFQ_DDA_ion_QExactive>`_ 
- `Label-free quantification of peptidoforms with DDA (QExactive) <https://proteobench.cubimed.rub.de/Quant_LFQ_DDA_peptidoform>`_ 
- `Label-free quantification of precursor ions with DDA (Astral) <https://proteobench.cubimed.rub.de/Quant_LFQ_DDA_ion_Astral>`_ 
- `Label-free quantification of precursor ions with DIA-PASEF <https://proteobench.cubimed.rub.de/Quant_LFQ_DIA_ion_diaPASEF>`_ 
- `Label-free quantification of precursor ions with DIA (Astral) <https://proteobench.cubimed.rub.de/Quant_LFQ_DIA_ion_Astral>`_ 
- `Label-free quantification of precursor ions with DIA (ZenoTOF 8600 - ZenoSWATH) <https://proteobench.cubimed.rub.de/Quant_LFQ_DIA_ion_ZenoTOF>`_ 

.. toctree::
   :maxdepth: 2
   :glob:
   :caption: Links to the documentation of active modules

   active-modules/index


Links to archived modules
=========================

- `Label-free quantification of precursor ions with DIA (AIF) <https://proteobench.cubimed.rub.de/Quant_LFQ_DIA_ion_AIF>`_: A discussion on oxidation-related issues with the data used for this module can be found `here <https://github.com/orgs/Proteobench/discussions/641>`_, and the documentation `here <archived-modules/4-quant-lfq-ion-dia-aif>`_.

.. toctree::
   :maxdepth: 2
   :glob:
   :caption: Links to documentation of archived modules

   archived-modules/index