MS/MS Data Compression Package

Description

This Python package is designed for efficient compression of Mass Spectrometry (MS/MS) data. It is based on the MassComp algorithm, which is described in the following paper: https://doi.org/10.1186/s12859-019-2962-7

Version

0.2.0

Features

• Delta and Hex Encoding: Efficiently encodes m/z values and intensities to optimize the compression.
• Brotli Compression: Utilizes Brotli, a high-performance compression algorithm, offering superior compression ratios and speeds compared to gzip.

Installation

To install the MS/MS Data Compression package, run:

pip install msms-compression

Usage

The package includes the following main compressor classes:

• SpectrumCompressorUrl: Utilizes URL-safe Base64 encoding.
• SpectrumCompressor: Uses Base85 encoding.

• Note: The m/z values must be sorted in ascending order before compression, and contain only positive values.

Example:

from msms_compression import SpectrumCompressorF32

# Sample data
mz_values, intensity_values = [100.0, 101.0, 102.0], [10.0, 20.0, 30.0]

# Initialize the compressor
compressor = SpectrumCompressorF32()

# Compress data
compressed_data = compressor.compress(mz_values, intensity_values)
print("Compressed Data:", compressed_data)

# Decompress data
decompressed_mz, decompressed_intensity = compressor.decompress(compressed_data)
assert decompressed_mz == mz_values
assert decompressed_intensity == intensity_values

Compression Strategy Comparison

The method compresses intensity values into two-character hexadecimal strings, offering 256 unique representations. This is a lossy approach, effectively reducing data size. Meanwhile, m/z values are compressed losslessly using delta encoding, maintaining their exact accuracy.