ProteomIQon
Version 2 (latest)

Version 2 (latest)

Version 1 (earliest)

Workflow Type: Common Workflow Language

Stable

The ProteomIQon is a collection of open source computational proteomics tools to build pipelines for the evaluation of MS derived proteomics data written in F#. The current state of the tool chain allows handle tasks like signal detection, peptide identification, quantification and protein inference. Each ProteomIQon tool is concerned with a specific task. This makes the tool-chain flexibel and easily extendable.

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SEEK ID: https://workflowhub.eu/workflows/2051?version=2

DOI: 10.48546/workflowhub.workflow.2051.2

Inputs

ID	Name	Description	Type
cores	CPU cores	Number of CPU cores to use for processing	int
inputMzML	MzML input directory	Input directory containing mzML files	Directory
inputPeptideDB	Peptide database file	Input peptide database file	File
outputAlignment	Alignment output directory	Output directory for alignment results	Directory
outputAlignmentQuant	Alignment quantification output directory	Output directory for alignment-based quantification	Directory
outputAlignmentStats	Alignment statistics output directory	Output directory for alignment statistics	Directory
outputDB	Database output directory	Output directory for database files	Directory
outputLabeledProt	Labeled protein output directory	Output directory for labeled protein quantification	Directory
outputMzML	MzML conversion output directory	Output directory for mzLite files	Directory
outputPSM	PSM output directory	Output directory for peptide-spectrum match files	Directory
outputPSMStats	PSM statistics output directory	Output directory for PSM statistics	Directory
outputProt	Protein output directory	Output directory for protein identification results	Directory
outputProtDeduced	Deduced protein output directory	Output directory for deduced protein results	Directory
outputQuant	Quantification output directory	Output directory for quantification results	Directory
outputQuantAndProt	Combined quantification and protein output directory	Output directory for combined quantification and protein results	Directory
paramsAlignmentBasedQuant	Alignment-based quantification parameters	Parameter file for alignment-based quantification	File
paramsAlignmentBasedQuantStats	Alignment quantification statistics parameters	Parameter file for alignment-based quantification statistics	File
paramsDB	Database parameters	Parameter file for database creation	File
paramsLabeledProteinQuant	Labeled protein quantification parameters	Parameter file for labeled protein quantification	File
paramsMzML	MzML parameters	Parameter file for mzML processing	File
paramsPSM	PSM parameters	Parameter file for PSM analysis	File
paramsPSMBasedQuant	PSM-based quantification parameters	Parameter file for PSM-based quantification	File
paramsPSMStats	PSM statistics parameters	Parameter file for PSM statistics	File
paramsProt	Protein inference parameters	Parameter file for protein inference	File

Steps

ID	Name	Description
AddDeducedPeptides	Add deduced peptides	Assigns protein inference information to peptides quantified via alignment, creating updated protein inference results for each quantification file
AlignmentBasedQuantStatistics	Alignment-based quantification statistics	Computes statistics and quality metrics for alignment-based quantification results
AlignmentBasedQuantification	Alignment-based quantification	Quantifies peptides transferred from other runs using alignment predictions with local dynamic time warping refinement and XIC extraction
JoinQuantPepIonsWithProteins	Join quantified peptide ions with proteins	Combines peptide quantification information with detailed protein inference results including q-values
LabeledProteinQuantification	Labeled protein quantification	Aggregates peptide-level quantification to protein-level, calculating ratios between light and heavy labeled peptides with optional charge and modification aggregation
MzMLToMzlite	MzML to mzLite conversion	Converts mzML files to mzLite format with optional peak picking and filtering of mass spectra
PSMBasedQuantification	PSM-based quantification	Performs XIC extraction and quantification of identified peptide ions using wavelet-based peak detection and Gaussian peak fitting, supporting both label-free and labeled quantification
PSMStatistics	PSM statistics and FDR control	Uses semi-supervised machine learning to integrate search engine scores into a consensus score and calculates local and global false discovery rates
PeptideDB	Peptide database creation	Creates a peptide database by in silico digestion of proteins from FASTA format, storing peptide-protein relationships in SQLite
PeptideSpectrumMatching	Peptide spectrum matching	Identifies MS/MS spectra by comparing them against peptides in the reference database using SEQUEST, Andromeda, and XTandem scoring
ProteinInference	Protein inference	Maps identified peptides to protein groups, handling one-to-many peptide-protein relationships and reporting peptide evidence classes
QuantBasedAlignment	Quantification-based alignment	Performs run alignment using smoothing splines to map retention times between source and target runs, enabling peptide ion transfer across runs

Outputs

ID	Name	Description	Type
alignment	Alignment results	Feature alignment results across samples	Directory
alignmentQuant	Alignment-based quantification	Quantification results based on feature alignment	Directory
alignmentStats	Alignment statistics	Statistical analysis of alignment-based quantification	Directory
db	Database files	Created database	Directory
labeledProteins	Labeled protein quantification	Labeled protein quantification results	Directory
mzml	mzLite files	Processed mzLite files	Directory
prot	Protein identification results	Protein inference and identification results	Directory
protDeduced	Deduced proteins	Deduced protein results from alignment-based quantification	Directory
psm	Peptide-spectrum matches	Peptide-spectrum match results	Directory
psmstats	PSM statistics	Statistical analysis of peptide-spectrum matches	Directory
quant	Quantification results	PSM-based quantification results	Directory
quantAndProt	Combined quantification and protein results	Combined quantification and protein inference results	Directory

Version History

Version 2 (latest) Created 20th Jan 2026 at 15:59 by Caroline Ott

fix ro-crate properties

Frozen Version-2 86bf0cf

Version 1 (earliest) Created 12th Jan 2026 at 14:46 by Caroline Ott

No revision comments

Frozen Version-1 33d9276

Creators and Submitter

Creators

Caroline Ott
David Zimmer

Submitter

Caroline Ott

Citation

Ott, C., & Zimmer, D. (2026). ProteomIQon. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.2051.2

License

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Activity

Views: 818 Downloads: 218

Created: 12th Jan 2026 at 14:46

Last updated: 20th Jan 2026 at 16:25

Annotated Properties

Topic annotations

Proteomics, Computational biology

Operation annotations

Protein quantification, Labeled quantification, Label-free quantification, Isotope-coded protein label

Scientific disciplines

Computer Science, Agricultural and Biological Sciences

ProteomIQon Version 2 (latest) Version 2 (latest) Version 1 (earliest)