Lyso-IP Ingestion

Installation

⬇️ Click here to install in Cauldron (requires Cauldron to be running)

Repository: https://github.com/noatgnu/lysoip-ingestion-plugin

Manual installation:

1. Open Cauldron
2. Go to Plugins → Install from Repository
3. Paste: https://github.com/noatgnu/lysoip-ingestion-plugin
4. Click Install

ID: lysoip-ingestion
Version: 1.0.0
Category: lysoip-qc
Author: CauldronGO Team

Description

Converts a Spectronaut, FragPipe, DIA-NN, or generic tidy search-engine export into the tidy long-format files the lysoip-* plugin suite consumes

Workflow Diagram

flowchart TD
    Start([Start]) --> step1
    step1["Reading sample sheet"]
    step1 --> parse
    parse["Parsing protein-level abundance"]
    parse --> has_peptides
    has_peptides{"Peptide file provided?"}
    has_peptides -->|"yes"| parse_peptides
    has_peptides -->|"no"| step2
    parse_peptides["Parsing peptide-level abundance"]
    parse_peptides --> step2
    step2["Ingestion complete"]
    step2 --> End([End])

Runtime

• Environments: python

• Entrypoint: lysoip_ingestion.py

Inputs

Input Details

Search Engine Format (format)

Which search engine produced the raw file

• Options: spectronaut (Spectronaut / DIA-NN long-format report), fragpipe (FragPipe combined_protein.tsv), diann (DIA-NN report.pg_matrix.tsv), generic_tidy (Generic tidy protein x sample matrix)

Protein-Level Raw File (raw_file)

Spectronaut/DIA-NN long report, FragPipe combined_protein.tsv, DIA-NN report.pg_matrix.tsv, or a generic tidy protein x sample matrix, matching the selected format

Peptide-Level Raw File (peptide_file)

Optional companion peptide-level file (report.pr_matrix.tsv for DIA-NN, combined_peptide.tsv for FragPipe, etc.). Enables downstream msqrob2-based differential expression instead of limma.

Sample Sheet (sample_sheet_file)

Maps each raw file's sample identifiers to an ip/wcl group and a replicate index

• Table Editor: Enabled with 3 columns
• Columns:
  • Sample: Sample (required)
  • Sample identifier matching a column/value in the raw file (e.g. R.FileName, or a FragPipe/DIA-NN column name)
  • Group: Group (required)
  • Must be exactly 'ip' or 'wcl'
  • ReplicateIndex: Replicate Index (required)
  • Biological replicate number within this sample's group

Require Proteotypic Peptides (require_proteotypic)

Drop peptides DIA-NN flags as shared across more than one protein; only relevant for the diann format

Outputs

Requirements

• Python Version: >=3.11

Package Dependencies (Inline)

Packages are defined inline in the plugin configuration:

• pandas>=2.0.0

Note: When you create a custom environment for this plugin, these dependencies will be automatically installed.

Example Data

This plugin includes example data for testing:

  format: diann
  raw_file: examples/diann_pg_matrix.tsv
  peptide_file: examples/diann_pr_matrix.tsv
  sample_sheet_file: examples/diann_sample_sheet.csv

Load example data by clicking the Load Example button in the UI.

Usage

Via UI

1. Navigate to lysoip-qc → Lyso-IP Ingestion
2. Fill in the required inputs
3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('lysoip-ingestion', {
  // Add parameters here
});