imspy-simulation 0.4.0

TimsTOF data simulation tools for proteomics.

imspy-simulation

TimsTOF data simulation tools for proteomics.

Installation

pip install imspy-simulation

For search integration (validation workflows):

pip install imspy-simulation[search]

Features

• Frame Builders: DIA and DDA frame simulation with annotation support
• TimSim: Complete simulation pipeline for synthetic timsTOF data
• Validation: Tools for validating simulated data against search results
• Isotope Simulation: Accurate isotope distribution generation
• TDF Writing: Write simulated data to Bruker TDF format

Quick Start

from imspy_simulation import (
    DIAFrameBuilder,
    DDAFrameBuilder,
    SimulationDatabase,
    TransmissionHandle,
    create_frame_builder,
    AcquisitionMode,
)

# Create a DIA frame builder
frame_builder = DIAFrameBuilder(
    database_path="path/to/synthetic_data.db",
    num_threads=16,
)

# Build frames
frames = frame_builder.build_frames([1, 2, 3])

CLI Tools

timsim

Full simulation pipeline:

timsim --config config.toml --output /path/to/output

Submodules

• builders/: Frame builder implementations (DIA, DDA)
• core/: Core protocols and wrappers
• data/: Simulation database and transmission handling
• timsim/: TimSim simulation pipeline
  • jobs/: Individual simulation steps
  • integration/: Integration workflows
  • validate/: Validation tools

Dependencies

• imspy-core: Core data structures (required)
• imspy-predictors: ML predictors for CCS, RT, intensity (required)
• imspy-search: Database search for validation (optional)

Related Packages

• imspy-core: Core data structures and timsTOF readers
• imspy-predictors: ML-based predictors
• imspy-search: Database search functionality
• imspy-vis: Visualization tools

License

MIT License - see LICENSE file for details.