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 Library Data Analysis

Associated Tutorial

This workflows is part of the tutorial Copy of PeptideDataAnalysis (imported from uploaded file), available in the GTN

Thanks to...

Tutorial Author(s): Jayadev Joshi, [Daniel ...

MaxQuant and MSstats for the analysis of label-free data

Associated Tutorial

This workflows is part of the tutorial Proteomics: MaxQuant and MSstats LFQ workflow, available in the GTN

Thanks to...

Tutorial Author(s): Melanie Föll, [Matthias ...

Proteogenomics 3: Novel peptide analysis

Associated Tutorial

This workflows is part of the tutorial GTN Proteogemics3 Novel Peptide Analysis, available in the GTN

Thanks to...

Tutorial Author(s): Subina Mehta, [Timothy J. ...

Biomarker candidate identification

Associated Tutorial

This workflows is part of the tutorial 'Biomarkers4Paris' Workflow, available in the GTN

Thanks to...

Tutorial Author(s): Florence Combes, David Christiany, ...

MaxQuant and MSstats for the analysis of TMT data

Associated Tutorial

This workflows is part of the tutorial MaxQuant MSstatsTMT Training, available in the GTN

Thanks to...

Tutorial Author(s): Klemens Fröhlich, [Melanie ...

DIA library Training HEK Ecoli data

Associated Tutorial

This workflows is part of the tutorial DIA_lib_OSW, available in the GTN

Thanks to...

Tutorial Author(s): Matthias Fahrner, Melanie Föll ...

metaquantome-function

Associated Tutorial

This workflows is part of the tutorial metaquantome-function-worklow, available in the GTN

Thanks to...

Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Associated Tutorial

This workflows is part of the tutorial Proteomics: Peptide and Protein Quantification via stable istobe labeling, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Detection and quantitation of N-termini (degradomics) via N-TAILS

Associated Tutorial

This workflows is part of the tutorial Tails Triple Dimethyl OpenMS2.1, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, [Björn ...

Annotating a protein list identified by LC-MS/MS experiments

Associated Tutorial

This workflows is part of the tutorial ProteoRE ProteomeAnnotation Tutorial (release 2.0), 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 'Proteome Annotation', available in the GTN

Thanks to...

Tutorial Author(s): Valentin Loux, [Florence ...

Protein FASTA Database Handling

Associated Tutorial

This workflows is part of the tutorial Proteomics: database handling, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, [Björn ...

Proteogenomics Galaxy Training Network Database Creation

Associated Tutorial

This workflows is part of the tutorial GTN Proteogenomics1 Database Creation, available in the GTN

Thanks to...

Tutorial Author(s): Subina Mehta, [Timothy J. ...

Protein FASTA Database Handling

Associated Tutorial

This workflows is part of the tutorial Proteomics: database handling including mycoplasma, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, [Björn ...

ML Modeling of Anti-cancer Peptides

Associated Tutorial

This workflows is part of the tutorial PeptideML, available in the GTN

Thanks to...

Tutorial Author(s): Jayadev Joshi, Daniel Blankenberg ...

Peptide and Protein ID using OpenMS tools

Associated Tutorial

This workflows is part of the tutorial Peptide And Protein ID Via OMS Using Two Search Engines, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, [Björn ...

Peptide and Protein ID using OpenMS tools

Associated Tutorial

This workflows is part of the tutorial Proteomics: Peptide and Protein ID using OpenMS, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, [Björn ...

Mass spectrometry imaging: Loading and exploring MSI data

Associated Tutorial

This workflows is part of the tutorial MS Imaging Loading Exploring Data, available in the GTN

Thanks to...

Tutorial Author(s): Melanie Föll, ...

DIA Analysis Training using HEK Ecoli data in OSW

Associated Tutorial

This workflows is part of the tutorial DIA_Analysis_OSW, available in the GTN

Thanks to...

Tutorial Author(s): Matthias Fahrner, Melanie Föll ...

metaquantome-data-creation

Associated Tutorial

This workflows is part of the tutorial metaQuantome_datacreation_workflow, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): [Subina ...

Peptide and Protein ID using SearchGUI and PeptideShaker

Associated Tutorial

This workflows is part of the tutorial Peptide And Protein ID Tutorial, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, [Björn ...

Peptide and Protein ID using SearchGUI and PeptideShaker

Associated Tutorial

This workflows is part of the tutorial ProteinID SG PS Tutorial WF datasetCollection, available in the GTN

Thanks to...

Tutorial Author(s): Florian Christoph Sigloch, [Björn ...

DIA MSstats Training export tabular

Associated Tutorial

This workflows is part of the tutorial DIA_analysis_MSstats, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): [Matthias ...

DIA MSstats Training msstats input tabular

Associated Tutorial

This workflows is part of the tutorial DIA_analysis_MSstats, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): [Matthias ...

Metaproteomics tutorial

Associated Tutorial

This workflows is part of the tutorial Metaproteomics_GTN, available in the GTN

Thanks to...

Tutorial Author(s): Timothy J. Griffin, Pratik Jagtap, ...

metaquantome-taxonomy

Associated Tutorial

This workflows is part of the tutorial metaquantome-taxonomy-workflow, available in the GTN

Thanks to...

Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...

Proteogenomics 2: Database Search

Associated Tutorial

This workflows is part of the tutorial GTN Proteogemics2 Database Search, available in the GTN

Thanks to...

Tutorial Author(s): Subina Mehta, [Timothy J. ...

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 ...

version 1.0, 160318, published at https://github.com/Stortebecker/secretome_prediction

Associated Tutorial

This workflows is part of the tutorial Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper, available in the GTN

Thanks to...

Tutorial Author(s): [Florian Christoph ...

Label-free data analysis using MaxQuant

Associated Tutorial

This workflows is part of the tutorial Proteomics: MaxQuant workflow, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): [Melanie ...

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Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Introduction

nfcore/diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data.

The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral library. If specified internal retention time standarts (irts) will be used to align library ...

nf-core/ddamsproteomics

Quantitative shotgun MS proteomics as done in Lehtio lab

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nf-core/ddamsproteomics pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local ...