Proteomics — Editorial Board Home

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Editorial Board

orcid logoMelanie Föll avatar Melanie Föllorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoSubina Mehta avatar Subina Mehtaorcid logoBjörn Grüning avatar Björn Grüning

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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to proteomics, protein identification, quantification and statistical modelling ❌ ✅
DIA Analysis using OpenSwathWorkflow ❌ ✅ ✅
EncyclopeDIA ❌ ✅
Label-free data analysis using MaxQuant ❌ ✅
Label-free versus Labelled - How to Choose Your Quantitation Method ✅ ❌
Library Generation for DIA Analysis ❌ ✅
MaxQuant and MSstats for the analysis of TMT data ❌ ✅
MaxQuant and MSstats for the analysis of label-free data ❌ ✅ ❌
Peptide and Protein ID using OpenMS tools ✅ ✅ ✅ ✅
Peptide and Protein ID using SearchGUI and PeptideShaker ✅ ✅
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) ✅ ✅ ✅
Protein FASTA Database Handling ✅ ❌
Annotating a protein list identified by LC-MS/MS experiments ❌ ✅
Biomarker candidate identification ❌ ❌
Secretome Prediction ✅ ✅
Single Cell Proteomics data analysis with bioconductor-scp ✅ ✅
Statistical analysis of DIA data ❌ ✅ ✅
Detection and quantitation of N-termini (degradomics) via N-TAILS ✅ ❌
Mass spectrometry imaging: Loading and exploring MSI data ✅ ✅
Metaproteomics tutorial ❌ ✅
Multiomics data analysis using MultiGSEA ✅ ✅
Proteogenomics 1: Database Creation ❌ ✅ ✅
Proteogenomics 2: Database Search ✅ ✅ ✅ ✅
Proteogenomics 3: Novel peptide analysis ❌ ✅ ✅
metaQuantome 1: Data creation ❌ ✅ ✅
metaQuantome 2: Function ❌ ✅ ✅ ✅
metaQuantome 3: Taxonomy ❌ ✅ ✅ ✅
Machine Learning Modeling of Anticancer Peptides ❌ ✅
Peptide Library Data Analysis ❌ ✅
Clinical Metaproteomics 1: Database-Generation ✅ ✅ ✅ ✅
Clinical Metaproteomics 2: Discovery ✅ ✅ ✅ ✅
Clinical Metaproteomics 3: Verification ✅ ✅ ✅ ✅
Clinical Metaproteomics 4: Quantitation ✅ ✅ ✅ ✅
Clinical Metaproteomics 5: Data Interpretation ✅ ✅ ✅ ✅
Neoantigen 1a: Fusion-Database-Generation ✅ ✅ ✅ ✅
Neoantigen 1b: Non-Reference-Database-Generation ✅ ✅ ✅ ✅
Neoantigen 2: Database merge and FragPipe discovery ✅ ✅ ✅ ✅
Neoantigen 3: PepQuery2 Verification ✅ ✅ ✅ ✅
Neoantigen 4: Variant Annotation ✅ ✅ ✅ ✅
Neoantigen 5a: Predicting HLA Binding ✅ ✅ ✅ ✅
Neoantigen 5b: IEDB binding Validated Neopeptides ✅ ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
DIA Analysis using OpenSwathWorkflow DIA_Analysis_OSW Feb 26, 2026 1 ❌ ❌ ❌
EncyclopeDIA EncyclopeDIA-GTN Feb 26, 2026 2 ✅ ✅ ❌
Label-free data analysis using MaxQuant Proteomics: MaxQuant workflow Feb 26, 2026 6 ✅ ❌ ❌
Library Generation for DIA Analysis DIA_lib_OSW Feb 26, 2026 1 ❌ ❌ ❌
MaxQuant and MSstats for the analysis of TMT data MaxQuant MSstatsTMT Training Feb 26, 2026 1 ❌ ❌ ❌
MaxQuant and MSstats for the analysis of label-free data Proteomics: MaxQuant and MSstats for the analysis of label-free data Feb 26, 2026 4 ❌ ✅ ❌
Peptide and Protein ID using OpenMS tools Proteomics: Peptide and Protein ID using OpenMS Feb 26, 2026 6 ❌ ❌ ❌
Peptide and Protein ID using OpenMS tools Peptide And Protein ID Via OMS Using Two Search Engines Feb 26, 2026 4 ❌ ❌ ❌
Peptide and Protein ID using SearchGUI and PeptideShaker Peptide And Protein ID Tutorial Feb 26, 2026 4 ❌ ❌ ❌
Peptide and Protein ID using SearchGUI and PeptideShaker ProteinID SG PS Tutorial WF datasetCollection Feb 26, 2026 4 ❌ ❌ ❌
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) Proteomics: Peptide and Protein Quantification via stable istobe labeling Feb 26, 2026 7 ✅ ❌ ❌
Protein FASTA Database Handling Proteomics: database handling Feb 26, 2026 5 ❌ ❌ ❌
Protein FASTA Database Handling Proteomics: database handling including mycoplasma Feb 26, 2026 6 ❌ ❌ ❌
Annotating a protein list identified by LC-MS/MS experiments 'Proteome Annotation' Feb 26, 2026 3 ❌ ❌ ❌
Annotating a protein list identified by LC-MS/MS experiments ProteoRE ProteomeAnnotation Tutorial (release 2.0) Feb 26, 2026 4 ❌ ❌ ❌
Biomarker candidate identification 'Biomarkers4Paris' Workflow Feb 26, 2026 3 ❌ ❌ ❌
Secretome Prediction Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper Feb 26, 2026 3 ❌ ❌ ❌
Statistical analysis of DIA data DIA_analysis_MSstats Feb 26, 2026 2 ✅ ❌ ❌
Statistical analysis of DIA data DIA_analysis_MSstats Feb 26, 2026 2 ✅ ❌ ❌
Detection and quantitation of N-termini (degradomics) via N-TAILS Tails Triple Dimethyl OpenMS2.1 Feb 26, 2026 4 ❌ ❌ ❌
Mass spectrometry imaging: Loading and exploring MSI data MS Imaging Loading Exploring Data Feb 26, 2026 4 ❌ ❌ ❌
Metaproteomics tutorial Metaproteomics_GTN Feb 26, 2026 7 ❌ ❌ ❌
Multiomics data analysis using MultiGSEA MultiGSEA Feb 26, 2026 1 ✅ ✅ ❌
Proteogenomics 1: Database Creation Proteogenomics 1: Database Creation Feb 26, 2026 10 ❌ ✅ ❌
Proteogenomics 2: Database Search Proteogenomics 2: Database Search Feb 26, 2026 8 ❌ ✅ ❌
Proteogenomics 3: Novel peptide analysis GTN Proteogemics3 Novel Peptide Analysis Feb 26, 2026 7 ❌ ✅ ❌
metaQuantome 1: Data creation metaQuantome_datacreation_workflow Feb 26, 2026 3 ✅ ❌ ❌
metaQuantome 2: Function metaquantome-function-worklow Feb 26, 2026 2 ❌ ❌ ❌
metaQuantome 3: Taxonomy metaquantome-taxonomy-workflow Feb 26, 2026 2 ❌ ❌ ❌
Machine Learning Modeling of Anticancer Peptides PeptideML Feb 26, 2026 1 ❌ ❌ ❌
Peptide Library Data Analysis Copy of PeptideDataAnalysis (imported from uploaded file) Feb 26, 2026 1 ❌ ❌ ❌
Clinical Metaproteomics 1: Database-Generation WF1_Database_Generation_Workflow Feb 26, 2026 1 ❌ ❌ ❌
Clinical Metaproteomics 2: Discovery WF2_Discovery-Workflow Feb 26, 2026 1 ❌ ❌ ❌
Clinical Metaproteomics 3: Verification WF3_VERIFICATION_WORKFLOW Feb 26, 2026 1 ❌ ❌ ❌
Clinical Metaproteomics 4: Quantitation WF4_Quantitation_Workflow Feb 26, 2026 1 ❌ ❌ ❌
Clinical Metaproteomics 5: Data Interpretation WF5_Data_Interpretation_Worklow Feb 26, 2026 1 ❌ ❌ ❌

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Learning Pathways using materials from this Topic

image of a 3D protein folding structure
Clinical metaproteomics workflows within Galaxy

This learning path aims to teach you the basics of how to perform metaproteomics analysis of the clinical data within the Galaxy platform. You will learn how to use Galaxy for analysis and will be guided through the most common first steps of any metaproteomics database generation to searching the database, verifying the proteins/peptides, and data analysis.

beginner proteomics
image of neoantigen mutation
Neoantigen discovery using the iPepGen pipeline

This learning path introduces a comprehensive immunopeptidogenomics (iPepGen) workflow for neoantigen discovery using label-free mass spectrometry data. The modules guide you through fusion and variant database generation, peptide identification with FragPipe, peptide validation using PepQuery2, and immunogenicity assessment through HLA binding predictions and IEDB screening.

intermediate immunopeptidomics cancer proteogenomics label-free
image of a 3D protein folding structure
Proteogenomics

This learning path aims to teach you the basics of how to perform proteogenomics analysis of the Mass spectrometry data within the Galaxy platform. You will learn how to use Galaxy for analysis and will be guided through the most common first steps of any proteogenomics database generation to searching the database, followed by novel peptide data analysis.

beginner proteomics
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Events using materials from this Topic

TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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