Proteomics agent for Lobster AI (DDA/DIA mass spectrometry, affinity platforms)

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  • License Expression: AGPL-3.0-or-later
    SPDX License Expression
  • Author: Omics-OS
  • Tags bioinformatics , proteomics , mass-spectrometry , DDA , DIA , Olink , SomaScan , lobster-ai
  • Requires: Python <3.14, >=3.12
  • Provides-Extra: network-analysis
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Project description

lobster-proteomics

Unified proteomics analysis for mass spectrometry (DDA/DIA) and affinity platforms (Olink, SomaScan).

Installation

pip install lobster-proteomics

Agents

Agent Description
proteomics_expert Full proteomics workflow orchestration with auto-detection of platform type and appropriate preprocessing.

Services

Service Purpose
ProteomicsAnalysisService Core analysis workflows for protein quantification
ProteomicsDifferentialService Differential protein expression between conditions
ProteomicsSurvivalService Survival analysis with protein biomarkers
ProteomicsNetworkService Protein-protein interaction network analysis
ProteomicsQualityService Quality control and missing value assessment
ProteomicsPreprocessingService MNAR/MAR-aware imputation and normalization
ProteomicsVisualizationService Volcano plots, heatmaps, and network graphs
MaxQuantParser Parse MaxQuant proteinGroups.txt output
DIANNParser Parse DIA-NN report.tsv output
SpectronautParser Parse Spectronaut report output
OlinkParser Parse Olink NPX export files

Features

  • Auto-detection of platform type from data characteristics
  • Missing value handling optimized for MNAR (mass spec) vs MAR (affinity) patterns
  • Platform-appropriate quality control with batch effect detection
  • Median and quantile normalization with log2 transformation
  • Multiple imputation strategies (MinDet, KNN, zero, median)
  • Differential protein analysis with multiple testing correction
  • Volcano plots and MA plots for results visualization
  • Protein-protein interaction network construction and visualization
  • Survival analysis integration for clinical proteomics studies
  • Support for multi-plex affinity platforms (Olink, SomaScan, Luminex)

Platform Support

Platform Missing Values Normalization Notes
Mass Spectrometry (DDA/DIA) 30-70% (MNAR) Median + log2 Peptide mapping support
Affinity (Olink) <30% (MAR) Quantile Plate effect correction
Affinity (SomaScan) <30% (MAR) Quantile Antibody validation

Requirements

  • Python 3.12+
  • lobster-ai >= 1.0.0

Tier Requirement

This is a free agent. Access is controlled at runtime via Lobster AI's tier system.

Documentation

Full documentation: docs.omics-os.com/docs/agents/proteomics

License

MIT

Project details

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  • License Expression: AGPL-3.0-or-later
    SPDX License Expression
  • Author: Omics-OS
  • Tags bioinformatics , proteomics , mass-spectrometry , DDA , DIA , Olink , SomaScan , lobster-ai
  • Requires: Python <3.14, >=3.12
  • Provides-Extra: network-analysis
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