{
  "id": "lib-process:bioinformatics--ms-proteomics-pipeline",
  "_kind": "LibraryProcess",
  "_file": "generated-library/processes.yaml",
  "_cluster": "generated-library",
  "attributes": {
    "displayName": "ms-proteomics-pipeline",
    "description": "Mass Spectrometry Proteomics Pipeline - Comprehensive pipeline for processing and\nanalyzing mass spectrometry-based proteomics data including protein identification, quantification,\nand statistical analysis.",
    "libraryPath": "library/specializations/domains/science/bioinformatics/ms-proteomics-pipeline.js",
    "specialization": "bioinformatics",
    "references": [
      "- MaxQuant: https://www.maxquant.org/\n- MSFragger: https://msfragger.nesvilab.org/\n- Perseus: https://maxquant.net/perseus/\n- Proteomics Standards Initiative: http://www.psidev.info/"
    ],
    "example": "const result = await orchestrate('specializations/domains/science/bioinformatics/ms-proteomics-pipeline', {\n  projectName: 'Proteome Profiling Study',\n  rawFiles: ['/data/sample1.raw', '/data/sample2.raw'],\n  database: 'UniProt_Human',\n  quantMethod: 'LFQ'\n});",
    "usesAgents": [
      "general-purpose"
    ]
  },
  "outgoingEdges": [
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "skill-area:data-analysis",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "skill-area:statistical-analysis",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 0.7
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "skill-area:python-data-pipelines",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 0.5
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "domain:bioinformatics",
      "kind": "lib_applies_to_domain",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "role:research-engineer",
      "kind": "lib_involves_role",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "role:biomedical-engineer",
      "kind": "lib_involves_role",
      "attributes": {
        "weight": 0.7
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "workflow:experiment-design",
      "kind": "lib_implements_workflow",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "specialization:biomedical-informatics",
      "kind": "lib_belongs_to_specialization",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--ms-proteomics-pipeline",
      "to": "specialization:bioinformatics",
      "kind": "lib_belongs_to_specialization",
      "attributes": {
        "weight": 0.9
      }
    }
  ],
  "incomingEdges": []
}