|
|
--- |
|
|
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. |
|
|
|
