MSFragger to CurtainPTM Converter

Version: 1.0.0

Commit Hash: 8fb277aed2bfec1fb03d26587f3e5ea8c5d4c821

Author: CauldronGO Team

Category: utilities

Subcategory: format-conversion

Convert MSFragger PTM single site output to CurtainPTM upload format. Extracts PTM positions from index columns, maps peptide sequences to proteins, 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

MSFragger to CurtainPTM Converter

Installation

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

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

Manual installation:

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

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

Description

Convert MSFragger PTM single site output to CurtainPTM upload format. Extracts PTM positions from index columns, maps peptide sequences to proteins, 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
input_file MSFragger Output File file Yes - Always visible
index_col Index Column Name text Yes Index Always visible
peptide_col Peptide Column Name text Yes Peptide Always visible
fasta_file FASTA File (Optional) file No - Always visible
get_position_from_peptide Parse Position from Peptide Column 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
sequence_window_size Sequence Window Size number (min: 1, max: 101, step: 2) No 21 Always visible

Input Details

MSFragger Output File (input_file)

MSFragger PTM output file containing differential analysis with site information in the Index column

Index Column Name (index_col)

Column name containing site information with accession ID and PTM position (e.g., P12345_S123)

  • Placeholder: Index

Peptide Column Name (peptide_col)

Column name containing peptide sequences

  • Placeholder: Peptide

FASTA File (Optional) (fasta_file)

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

Parse Position from Peptide Column (get_position_from_peptide)

Enable this to extract PTM position from lowercase residues in the peptide sequence instead of the index column

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

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 → MSFragger to CurtainPTM Converter
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

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