Teams: Australian BioCommons, Galaxy Australia, ELIXIR Training, ELIXIR Tools platform, National Computational Infrastructure (NCI) WorkflowHub team
Organizations: University of Melbourne, Australian BioCommons

Expertise: Biochemistry, Proteomics, Mass Spectrometry Imaging
Tools: Mass spectrometry, Proteomics
encyclopedia- DIA Metaproteomics
Associated Tutorial
This workflows is part of the tutorial EncyclopeDIA, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Proteogenomics 3: Novel peptide analysis
Associated Tutorial
This workflows is part of the tutorial Proteogenomics 3: Novel peptide analysis, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
...
DIA Analysis Training using HEK Ecoli data in OSW
Associated Tutorial
This workflows is part of the tutorial DIA Analysis using OpenSwathWorkflow, available in the GTN
Thanks to...
Tutorial Author(s): Matthias Fahrner, [Melanie ...
DIA MSstats Training msstats input tabular
Associated Tutorial
This workflows is part of the tutorial Statistical analysis of DIA data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Matthias ...
metaquantome-taxonomy
Associated Tutorial
This workflows is part of the tutorial metaQuantome 3: Taxonomy, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...
DIA MSstats Training export tabular
Associated Tutorial
This workflows is part of the tutorial Statistical analysis of DIA data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Matthias ...
Mass spectrometry imaging: Loading and exploring MSI data
Associated Tutorial
This workflows is part of the tutorial Mass spectrometry imaging: Loading and exploring MSI data, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, ...
ML Modeling of Anti-cancer Peptides
Associated Tutorial
This workflows is part of the tutorial Machine Learning Modeling of Anticancer Peptides, available in the GTN
Thanks to...
Tutorial Author(s): Jayadev Joshi, [Daniel ...
metaquantome-function
Associated Tutorial
This workflows is part of the tutorial metaQuantome 2: Function, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...
metaquantome-data-creation
Associated Tutorial
This workflows is part of the tutorial metaQuantome 1: Data creation, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Subina ...
Peptide and Protein ID using OpenMS tools
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using OpenMS tools, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein Quantification via Stable Isotope Labelling (SIL), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Label-free data analysis using MaxQuant
Associated Tutorial
This workflows is part of the tutorial Label-free data analysis using MaxQuant, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Melanie ...
Peptide and Protein ID using OpenMS tools
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using OpenMS tools, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Metaproteomics tutorial
Associated Tutorial
This workflows is part of the tutorial Metaproteomics tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Timothy J. Griffin, Pratik Jagtap, ...
Protein FASTA Database Handling
Associated Tutorial
This workflows is part of the tutorial Protein FASTA Database Handling, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Protein FASTA Database Handling
Associated Tutorial
This workflows is part of the tutorial Protein FASTA Database Handling, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Detection and quantitation of N-termini (degradomics) via N-TAILS
Associated Tutorial
This workflows is part of the tutorial Detection and quantitation of N-termini (degradomics) via N-TAILS, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
DIA library Training HEK Ecoli data
Associated Tutorial
This workflows is part of the tutorial Library Generation for DIA Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Matthias Fahrner, Melanie Föll ...
version 1.0, 160318, published at https://github.com/Stortebecker/secretome_prediction
Associated Tutorial
This workflows is part of the tutorial Secretome Prediction, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
Annotating a protein list identified by LC-MS/MS experiments
Associated Tutorial
This workflows is part of the tutorial Annotating a protein list identified by LC-MS/MS experiments, available in the GTN
Thanks to...
Tutorial Author(s): Valentin Loux, [Florence ...
Annotating a protein list identified by LC-MS/MS experiments
Associated Tutorial
This workflows is part of the tutorial Annotating a protein list identified by LC-MS/MS experiments, available in the GTN
Thanks to...
Tutorial Author(s): Valentin Loux, [Florence ...
Biomarker candidate identification
Associated Tutorial
This workflows is part of the tutorial Biomarker candidate identification, available in the GTN
Thanks to...
Tutorial Author(s): Florence Combes, [David ...
MaxQuant and MSstats for the analysis of TMT data
Associated Tutorial
This workflows is part of the tutorial MaxQuant and MSstats for the analysis of TMT data, available in the GTN
Thanks to...
Tutorial Author(s): Klemens Fröhlich, [Melanie ...
Peptide and Protein ID using SearchGUI and PeptideShaker
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using SearchGUI and PeptideShaker, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
Peptide and Protein ID using SearchGUI and PeptideShaker
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using SearchGUI and PeptideShaker, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
Peptide Library Data Analysis
Associated Tutorial
This workflows is part of the tutorial Peptide Library Data Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Jayadev Joshi, [Daniel ...
KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Armed with PRICKLE(3)s: Stabilizing WNT/PCP complexes against RNF43-mediated ubiquitination". Workflow was built using the KNIME software container environment, version 4.7.7a, which can be created using "docker pull cfprot/knime:4.7.7a" command in Docker. The input data for the KNIME workflow (the report.tsv from DIA-NN) can be found on PRIDE repository under the identifier PXD057854.
A R workflow for proteomics data analysis is reported. This pipeline was basing on protein expression projects, stored on the PRIDE database and reported on the COVID-19 Data portal. This is an R pipeline to analyze protein expression data, built on lung cell lines infected by SARS-CoV-2 variants: B.1, Delta, and Omicron BA.1 (Mezler et al. 2023) https://www.ebi.ac.uk/pride/archive/projects/PXD037265. This pipeline can obtain DEPs for each variant, starting from normalized protein expression ...
KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Proximity interactomics identifies RAI14, EPHA2 and PHACTR4 as essential components of Wnt/planar cell polarity pathway in vertebrates". Workflow was built using the KNIME software container environment, version 4.7.7a, which can be created using "docker pull cfprot/knime:4.7.7a" command in Docker. The input data for the KNIME workflow (the report.tsv from DIA-NN) can be found on PRIDE repository under ...
Quantitative Mass Spectrometry nf-core workflow
Proteomics label-free quantification (LFQ) analysis pipeline using OpenMS and MSstats, with feature quantification, feature summarization, quality control and group-based statistical analysis.
Type: Nextflow
Creators: Julianus Pfeuffer, Lukas Heumos, Leon Bichmann, Timo Sachsenberg, Yasset Perez-Riverol
Submitter: WorkflowHub Bot
Proteogenomics database creation workflow using pypgatk framework.
Automated quantitative analysis of DIA proteomics mass spectrometry measurements.
ProGFASTAGen
The ProGFASTAGen (Protein-Graph-FASTA-Generator or ProtGraph-FASTA-Generator) repository contains workflows to generate so-called precursor-specific-FASTAs (using the precursors from MGF-files) including feature-peptides, like VARIANTs or CONFLICTs if desired, or global-FASTAs (as described in ProtGraph). The single workflow scripts have been implemented with Nextflow-DSL-2 ...
Introduction
wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...
Type: Nextflow
Creators: Veit Schwämmle, Magnus Palmblad
Submitters: Laura Rodriguez-Navas, José Mª Fernández
Joint multi-omics dimensionality reduction approaches for CAKUT data using peptidome and proteome data
Brief description In (Cantini et al. 2020), Cantini et al. evaluated 9 representative joint dimensionality reduction (jDR) methods for multi-omics integration and analysis and . The methods are Regularized Generalized Canonical Correlation Analysis (RGCCA), Multiple co-inertia analysis (MCIA), Multi-Omics Factor Analysis (MOFA), Multi-Study Factor Analysis (MSFA), iCluster, Integrative NMF ...
Type: Snakemake
Creators: Ozan Ozisik, Juma Bayjan, Cenna Doornbos, Friederike Ehrhart, Matthias Haimel, Laura Rodriguez-Navas, José Mª Fernández, Eleni Mina, Daniël Wijnbergen
Submitter: Juma Bayjan
In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.
The peptidome and ...
Type: Snakemake
Creators: Woosub Shin, Friederike Ehrhart, Juma Bayjan, Cenna Doornbos, Ozan Ozisik
Submitter: Juma Bayjan
ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin
Submitter: Patrick Durand