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license: unknown
task_categories:
- other
tags:
- mass-spectrometry
- proteomics
- metabolomics
- mscompress
size_categories:
- n<1K
---
# My MSZ Dataset
A dataset containing mass spectrometry data in MSZ format.
## Dataset Information
- **Format**: MSZ (compressed mass spectrometry)
- **Number of files**: 1
- **Granularity**: spectrum-level
- **Filter**: All MS levels
## Files
- `test.msz`
## Usage
This dataset requires the `mscompress` library to load the MSZ files.
### Installation
```bash
pip install mscompress
```
### Loading the Dataset
```python
from datasets import load_dataset
# Load the dataset
dataset = load_dataset("my-msz-dataset")
# Access spectra
for example in dataset["train"]:
mz = example["mz"]
intensity = example["intensity"]
print(f"Spectrum {example['scan_number']}: {len(mz)} peaks")
```
### Direct MSZ File Access
For more control, you can download and read the MSZ files directly:
```python
import mscompress
from huggingface_hub import hf_hub_download
# Download an MSZ file
msz_path = hf_hub_download(
repo_id="<repo_id>",
filename="data/test.msz",
repo_type="dataset"
)
# Read with mscompress
msz = mscompress.read(msz_path)
# Access spectra with random access
spectrum = msz.spectra[0]
print(f"m/z: {spectrum.mz}")
print(f"Intensity: {spectrum.intensity}")
```
## Dataset Structure
### Spectrum-level Features
- `source_file`: Name of the source MSZ file
- `spectrum_index`: Index of the spectrum in the file
- `scan_number`: Scan number from the instrument
- `ms_level`: MS level (1 for MS1, 2 for MS2/MS3, etc.)
- `retention_time`: Retention time in seconds
- `num_peaks`: Number of m/z-intensity pairs
- `mz`: Array of m/z values
- `intensity`: Array of intensity values
## Citation
If you use this dataset, please cite the mscompress library:
```
@software{mscompress,
title = {mscompress: High-performance compression for mass spectrometry data},
url = {https://github.com/chrisagrams/mscompress}
}
```
## License
Please check with the dataset creator for license information.
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