JAMSS

JAMSS simulates mass spectrometry (MS) and liquid chromatography-mass spectrometry (LC-MS) runs with known identities and quantities to provide labeled proteomics datasets for evaluating and developing data processing algorithms.

Key Features:

• Simulated MS and LC-MS runs: Generates in silico mass spectrometry (MS) and liquid chromatography-mass spectrometry (LC-MS) runs with known identities and quantities.
• Labeled proteomics datasets: Produces labeled proteomics data suitable for algorithm evaluation and benchmarking.
• Multithreading capability: Uses multithreading to parallelize simulation computations and handle complex simulations.
• Retention time shift model: Incorporates a retention time shift model to mimic variations in experimental LC-MS retention times.
• Reproducibility and provenance meta-information: Records provenance and meta-information for reproducibility of simulated signals.
• Output format: Exports simulated data in mzML 1.1.0 format.

Scientific Applications:

• Algorithm development and benchmarking: Provides ground-truth labeled datasets for developing and benchmarking proteomics data processing algorithms.
• Validation of analysis pipelines: Enables validation of existing data processing and quantification pipelines using controlled simulated data.
• Method testing and theoretical exploration: Supports testing of novel methodologies and exploration of theoretical experimental scenarios without physical experiments.

Methodology:

Simulates MS and LC-MS runs with known identities and quantities, applies a retention time shift model, performs simulations using multithreading, records provenance/meta-information, and exports results in mzML 1.1.0 format.