Skip to content

DIANN

Jump to bottom
Charlie Bayne edited this page Oct 16, 2025 · 3 revisions

DIA-NN

Conduit relies on DIA-NN for spectral matching and quantification.
DIA-NN performs the core computational tasks of matching MS/MS spectra to peptides and estimating peptide abundances.

For background, see the original DIA-NN publication:

Demichev et al., Nature Methods (2019) — https://www.nature.com/articles/s41592-019-0638-x

DIA-NN is integrated into Conduit in two main steps:

  1. Generating a spectral library
  2. Running the DIA-NN search

Generating a Spectral Library

This step involves predicting retention times and spectral properties for in silico–digested peptides.
DIA-NN internally uses deep learning–based spectral predictors Prosit- sytle models to estimate fragment ion intensities and retention times.

Conduit allows users to customize this step using any flags or parameters supported by DIA-NN’s command-line interface:
👉 DIA-NN Command-Line Reference

By default:

  • The file generate_diann_spectral_library.cfg from the top-level configuration directory is copied to your experiment-specific config folder.
  • This default file contains sensible baseline parameters suitable for most experiments.

For fine-grained control, you can provide your own generate_diann_spectral_library.cfg in your experiment’s config directory.
Conduit will automatically use your version instead of the default.

Running a DIA-NN Search

Once the spectral library is generated, DIA-NN is run to search the experimental MS data and identify peptide-spectrum matches (PSMs).

Similar to the spectral library generation step, Conduit gives users full control over the search parameters — any command-line flag accepted by DIA-NN can be used.

By default:

  • The file run_diann.cfg from the top-level configuration directory is copied into your experiment-specific config directory.
  • This file includes default parameters designed for robust and reproducible results.

For more detailed customization, you can supply your own run_diann.cfg file with arbitrary values.
Conduit will use your configuration to control how DIA-NN performs the search.

In summary:
Conduit provides robust defaults for both DIA-NN spectral library generation and searching, while allowing full parameter transparency and user control for advanced workflows.

Clone this wiki locally