Finalize

.python-version

@@ -0,0 +1 @@
+3.14

README.md

@@ -12,6 +12,9 @@ Generate a spectral library for [Spectronaut](https://biognosys.com/software/spe
   - Alternatively you can also use [uv](https://docs.astral.sh/uv/getting-started/installation/).
 - We recommend at least 32 GB of memory for larger MS files!
 
+> [!NOTE]
+> Pinned python and package versions are available in the `uv.lock` file!
+
 ## Usage
 
 > [!IMPORTANT]
@@ -33,6 +36,76 @@ Generate a spectral library for [Spectronaut](https://biognosys.com/software/spe
 - The full spectral library including all target and decoy annotations is created with extension `_spectralLibraryFULL.csv`.
   - This spectral library should be used with [Spectronaut](https://biognosys.com/software/spectronaut/)!
 
+## Example
+
+Here is a minimal example (we are using [uv](https://docs.astral.sh/uv/) here):
+
+- You can download some example data from [here](http://u.pc.cd/omH).
+- Clone this repository:
+  ```bash
+  git clone https://github.com/hgb-bin-proteomics/MSAnnika_Spectral_Library_exporter.git 
+  ```
+- Extract the example data into the `MSAnnika_Spectral_Library_exporter` folder.
+  - **Overwrite any files if prompted!**
+- Go into the `MSAnnika_Spectral_Library_exporter` folder.
+- The folder should contain the example files:
+  - `config.py`
+  - `XLpeplib_Beveridge_QEx-HFX_DSS_R2.mzML`
+  - `XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs.xlsx`
+- Now run the spectral library creation script with [uv](https://docs.astral.sh/uv/):
+  ```bash
+  uv run create_spectral_library.py
+  ```
+- The script should run for about one minute and you should see output like this:
+  <details><summary>Expand for output!</summary>
+
+  ```text
+  INFO: Spectral library creation started at 2026-05-12 15:34:30.616870.
+  INFO: Creating spectral library with input files:
+  Spectra:
+  XLpeplib_Beveridge_QEx-HFX_DSS_R2.mzML
+  CSMs: XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs.xlsx
+  INFO: Using the following modifications:
+  {'Oxidation': [15.994915], 'Carbamidomethyl': [57.021464], 'DSSO': [54.01056, 85.98264, 103.9932], 'DSS': [138.06808]}
+  INFO: Using the following ion types:
+  ('b', 'y')
+  INFO: Using the following charge states:
+  [1, 2, 3, 4]
+  INFO: Using a match tolerance of: 0.02 Da
+  INFO: Starting annotation process...
+  INFO: Reading CSMs...
+  INFO: Done reading CSMs! Filtering for unique residue pairs...
+  INFO: Done filtering for unique residue pairs!
+  INFO: Sorting CSMs...
+  INFO: Finished sorting CSMs! Starting spectral library creation...
+  INFO: Processing CSMs...:   0%|      | 0/382 [00:00<?, ?it/s]Found unseen spectrum file! Trying to read spectrum file...
+  Reading mzML file...
+  Found 0/10951 spectra without peaks in file XLpeplib_Beveridge_QEx-HFX_DSS_R2.mzML!
+  INFO: Read all spectra from file XLpeplib_Beveridge_QEx-HFX_DSS_R2.mzML.
+  INFO: Read 1/1 files...
+  INFO: Read all spectra files successfully!
+  INFO: Processing CSMs...: 100%|██████| 382/382 [00:14<00:00, 27.15it/s]
+  SUCCESS: Spectral library created with filename:
+  XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibrary.csv
+  SUCCESS: Decoy Spectral libraries created with filenames:
+  XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryDECOY_DD.csv
+  XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryDECOY_DT.csv
+  XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryDECOY_TD.csv
+  Creating merged library...
+  SUCCESS: Merged spectral library created with filename:
+  XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryFULL.csv
+  SUCCESS: Spectral library creation finished at 2026-05-12 15:34:45.473506.
+  ```
+
+  </details>
+- You should see the following files created:
+  - `XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibrary.csv` ➡️ Target(-Target) spectral library
+  - `XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryDECOY_DD.csv` ➡️ Decoy-Decoy spectral library
+  - `XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryDECOY_DT.csv` ➡️ Decoy-Target spectral library
+  - `XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryDECOY_TD.csv` ➡️ Target-Decoy spectral library
+  - `XLpeplib_Beveridge_QEx-HFX_DSS_R2_CSMs_spectralLibraryFULL.csv` ➡️ Full spectral library
+- The full library can now be used in Spectronaut!
+
 ## Usage with xiSearch + xiFDR
 
 Starting with version [1.4.4](https://github.com/hgb-bin-proteomics/MSAnnika_Spectral_Library_exporter/releases/tag/v1.4.4) this script also supports input from

pyproject.toml

@@ -0,0 +1,12 @@
+[project]
+name = "msannika-spectral-library-exporter"
+version = "1.4.22"
+description = "Generate a spectral library for Spectronaut from MS Annika results."
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "openpyxl>=3.1.5",
+    "pandas>=3.0.3",
+    "pyteomics[xml]>=4.7.5",
+    "tqdm>=4.67.3",
+]