SynProtX

An official implementation of our research paper "SynProtX: A Large-Scale Proteomics-Based Deep Learning Model for Predicting Synergistic Anticancer Drug Combinations".

SynProtX is a deep learning model that integrates large-scale proteomics data, molecular graphs, and chemical fingerprints to predict synergistic effects of anticancer drug combinations. It provides robust ...

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, ...

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 ...

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 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 ...

[![Cite ...

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.

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 ...

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 ...

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 ...

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.