DIA-NN to CurtainPTM Converter

Version: 1.0.0

Commit Hash: acad6cffac5cbb34e73528aaad20abc2eb453164

Author: CauldronGO Team

Category: utilities

Subcategory: format-conversion

Convert DIA-NN PTM differential analysis output to CurtainPTM upload format. Processes modified sequences, maps PTM positions to protein sequences, and generates sequence windows around modification sites. Based on: Phung et al. (2024) PNAS 121(7):e2312676121. Repository: https://github.com/noatgnu/curtain-utils

Install with Cauldron get_app
README

DIA-NN to CurtainPTM Converter

Installation

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

Repository: https://github.com/noatgnu/diann-curtainptm-converter-plugin

Manual installation:

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

ID: diann-curtainptm-converter
Version: 1.0.0
Category: utilities
Author: CauldronGO Team

Description

Convert DIA-NN PTM differential analysis output to CurtainPTM upload format. Processes modified sequences, maps PTM positions to protein sequences, and generates sequence windows around modification sites. Based on: Phung et al. (2024) PNAS 121(7):e2312676121. Repository: https://github.com/noatgnu/curtain-utils

Runtime

  • Environments: python

  • Entrypoint: convert.py

Inputs

Name Label Type Required Default Visibility
pr_file PR File (Differential Analysis) file Yes - Always visible
report_file Report File (Optional) file No - Always visible
modification_type Modification Type text Yes UniMod:21 Always visible
fasta_file FASTA File (Optional) file No - Always visible
localization_score_col Localization Score Column text No PTM.Site.Confidence Always visible
multiple_site Process Multiple Sites boolean No false Always visible
uniprot_columns UniProt Data Columns text No accession,id,sequence,protein_name Always visible
output_filename Output Filename text No curtainptm_input.txt Always visible
output_meta Output Metadata File boolean No false Conditional
sequence_window_size Sequence Window Size number (min: 1, max: 101, step: 2) No 21 Always visible

Input Details

PR File (Differential Analysis) (pr_file)

DIA-NN precursor-level differential analysis file containing Modified.Sequence, Precursor.Id, and Protein.Group columns

Report File (Optional) (report_file)

DIA-NN report file containing protein sequences and PTM.Site.Confidence scores

Modification Type (modification_type)

Type of modification to process using UniMod identifier (e.g., UniMod:21 for Phosphorylation, UniMod:1 for Acetylation, UniMod:35 for Oxidation, UniMod:4 for Carbamidomethyl)

  • Placeholder: UniMod:21

FASTA File (Optional) (fasta_file)

Protein sequence FASTA file. If not provided, sequences will be fetched from UniProt automatically.

Localization Score Column (localization_score_col)

Column name containing PTM site confidence scores in the report file

  • Placeholder: PTM.Site.Confidence

Process Multiple Sites (multiple_site)

Enable this to process peptides with multiple modification sites. When enabled, all sites will be reported in semicolon-separated format.

UniProt Data Columns (uniprot_columns)

Comma-separated list of UniProt columns to retrieve when fetching sequences online

  • Placeholder: accession,id,sequence,protein_name

Output Filename (output_filename)

Name of the output file (will be created in the output folder)

  • Placeholder: curtainptm_input.txt

Output Metadata File (output_meta)

Generate an additional metadata file with intensity information from the report file. Only works when a report file is provided.

Sequence Window Size (sequence_window_size)

Size of the sequence window around modification sites (must be odd number). Default is 21 (10 residues before + modification + 10 after).

Outputs

Name File Type Format Description
converted_file *.txt data tsv Converted file in CurtainPTM upload format with PTM positions, sequence windows, and protein annotations

Requirements

  • Python Version: >=3.10

Python Dependencies (External File)

Dependencies are defined in: requirements.txt

  • curtainutils>=0.1.24
  • pandas>=2.0.0
  • click>=8.0.0

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

Usage

Via UI

  1. Navigate to utilities → DIA-NN to CurtainPTM Converter
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('diann-curtainptm-converter', {
  // Add parameters here
});