Spectronaut to CurtainPTM Converter

Version: 1.0.0

Commit Hash: 0b49ca3b06ac43f1db2a56ebbc8fa4b69f1e82ee

Author: CauldronGO Team

Category: utilities

Subcategory: format-conversion

Convert Spectronaut PTM output to CurtainPTM upload format. Supports multiple processing modes for different data formats - basic PTM processing, PTM group processing with site probabilities, and ProForma sequence processing with position validation. Based on: Phung et al. (2024) PNAS 121(7):e2312676121. Repository: https://github.com/noatgnu/curtain-utils

Install with Cauldron get_app
README

Spectronaut to CurtainPTM Converter

Installation

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

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

Manual installation:

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

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

Description

Convert Spectronaut PTM output to CurtainPTM upload format. Supports multiple processing modes for different data formats - basic PTM processing, PTM group processing with site probabilities, and ProForma sequence processing with position validation. 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 Spectronaut Output File file Yes - Always visible
index_col Index Column Name text Yes PTM_collapse_key Always visible
peptide_col Peptide Column Name text Yes PEP.StrippedSequence Always visible
uniprot_id_col UniProt ID Column Name text No UniprotID Always visible
processing_mode Processing Mode select (1, 2, 3) Yes 1 Always visible
modification_type Modification Type (Modes 2 & 3) text No Phospho (STY) Visible when processing_mode is one of: 2, 3
fasta_file FASTA File (Optional) file No - 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

Spectronaut Output File (input_file)

Spectronaut PTM output file containing differential analysis data

Index Column Name (index_col)

Column name containing position information in the format _X123_* where X is the residue and 123 is the position

  • Placeholder: PTM_collapse_key

Peptide Column Name (peptide_col)

Column name containing peptide sequences (format depends on processing mode)

  • Placeholder: PEP.StrippedSequence

UniProt ID Column Name (uniprot_id_col)

Column name containing UniProt accession IDs

  • Placeholder: UniprotID

Processing Mode (processing_mode)

Processing mode selection: Mode 1: Basic PTM processing with position extraction from index column Mode 2: PTM group processing with site probability calculations Mode 3: ProForma sequence processing with enhanced position validation

  • Options: 1, 2, 3

Modification Type (Modes 2 & 3) (modification_type)

Type of modification to process (e.g., Phospho (STY), Acetyl (K), Methyl (K)). Only used in modes 2 and 3.

  • Placeholder: Phospho (STY)

FASTA File (Optional) (fasta_file)

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

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

Via Plugin System

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