Proteomics — Editorial Board Home

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Editorial Board

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

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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 PepQuery Validated Neopeptides ✅ ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
DIA Analysis using OpenSwathWorkflow DIA_Analysis_OSW Jul 17, 2025 1 ❌ ❌ ❌
EncyclopeDIA EncyclopeDIA-GTN Jul 17, 2025 2 ✅ ✅ ❌
Label-free data analysis using MaxQuant Proteomics: MaxQuant workflow Jul 17, 2025 6 ✅ ❌ ❌
Library Generation for DIA Analysis DIA_lib_OSW Jul 17, 2025 1 ❌ ❌ ❌
MaxQuant and MSstats for the analysis of TMT data MaxQuant MSstatsTMT Training Jul 17, 2025 1 ❌ ❌ ❌
MaxQuant and MSstats for the analysis of label-free data Proteomics: MaxQuant and MSstats for the analysis of label-free data Jul 17, 2025 4 ❌ ✅ ❌
Peptide and Protein ID using OpenMS tools Proteomics: Peptide and Protein ID using OpenMS Jul 17, 2025 6 ❌ ❌ ❌
Peptide and Protein ID using OpenMS tools Peptide And Protein ID Via OMS Using Two Search Engines Jul 17, 2025 4 ❌ ❌ ❌
Peptide and Protein ID using SearchGUI and PeptideShaker Peptide And Protein ID Tutorial Jul 17, 2025 4 ❌ ❌ ❌
Peptide and Protein ID using SearchGUI and PeptideShaker ProteinID SG PS Tutorial WF datasetCollection Jul 17, 2025 4 ❌ ❌ ❌
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) Proteomics: Peptide and Protein Quantification via stable istobe labeling Jul 17, 2025 7 ✅ ❌ ❌
Protein FASTA Database Handling Proteomics: database handling Jul 17, 2025 5 ❌ ❌ ❌
Protein FASTA Database Handling Proteomics: database handling including mycoplasma Jul 17, 2025 6 ❌ ❌ ❌
Annotating a protein list identified by LC-MS/MS experiments 'Proteome Annotation' Jul 17, 2025 3 ❌ ❌ ❌
Annotating a protein list identified by LC-MS/MS experiments ProteoRE ProteomeAnnotation Tutorial (release 2.0) Jul 17, 2025 4 ❌ ❌ ❌
Biomarker candidate identification 'Biomarkers4Paris' Workflow Jul 17, 2025 3 ❌ ❌ ❌
Secretome Prediction Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper Jul 17, 2025 3 ❌ ❌ ❌
Statistical analysis of DIA data DIA_analysis_MSstats Jul 17, 2025 2 ✅ ❌ ❌
Statistical analysis of DIA data DIA_analysis_MSstats Jul 17, 2025 2 ✅ ❌ ❌
Detection and quantitation of N-termini (degradomics) via N-TAILS Tails Triple Dimethyl OpenMS2.1 Jul 17, 2025 4 ❌ ❌ ❌
Mass spectrometry imaging: Loading and exploring MSI data MS Imaging Loading Exploring Data Jul 17, 2025 4 ❌ ❌ ❌
Metaproteomics tutorial Metaproteomics_GTN Jul 17, 2025 7 ❌ ❌ ❌
Multiomics data analysis using MultiGSEA MultiGSEA Jul 17, 2025 1 ✅ ✅ ❌
Proteogenomics 1: Database Creation Proteogenomics 1: Database Creation Jul 17, 2025 10 ❌ ✅ ❌
Proteogenomics 2: Database Search Proteogenomics 2: Database Search Jul 17, 2025 8 ❌ ✅ ❌
Proteogenomics 3: Novel peptide analysis GTN Proteogemics3 Novel Peptide Analysis Jul 17, 2025 7 ❌ ✅ ❌
metaQuantome 1: Data creation metaQuantome_datacreation_workflow Jul 17, 2025 3 ✅ ❌ ❌
metaQuantome 2: Function metaquantome-function-worklow Jul 17, 2025 2 ❌ ❌ ❌
metaQuantome 3: Taxonomy metaquantome-taxonomy-workflow Jul 17, 2025 2 ❌ ❌ ❌
Machine Learning Modeling of Anticancer Peptides PeptideML Jul 17, 2025 1 ❌ ❌ ❌
Peptide Library Data Analysis Copy of PeptideDataAnalysis (imported from uploaded file) Jul 17, 2025 1 ❌ ❌ ❌
Clinical Metaproteomics 1: Database-Generation WF1_Database_Generation_Workflow Jul 17, 2025 1 ❌ ❌ ❌
Clinical Metaproteomics 2: Discovery WF2_Discovery-Workflow Jul 17, 2025 1 ❌ ❌ ❌
Clinical Metaproteomics 3: Verification WF3_VERIFICATION_WORKFLOW Jul 17, 2025 1 ❌ ❌ ❌
Clinical Metaproteomics 4: Quantitation WF4_Quantitation_Workflow Jul 17, 2025 1 ❌ ❌ ❌
Clinical Metaproteomics 5: Data Interpretation WF5_Data_Interpretation_Worklow Jul 17, 2025 1 ❌ ❌ ❌
Neoantigen 1a: Fusion-Database-Generation Gigascience_Fusions_demonstration_STS26T-Gent_Workflow Jul 17, 2025 1 ❌ ✅ ❌
Neoantigen 1b: Non-Reference-Database-Generation Gigascience_Indels_SAV_non-reference_demonstration_STS26T-Gent_Workflow Jul 17, 2025 1 ❌ ✅ ❌
Neoantigen 2: Database merge and FragPipe discovery GigaScience_Database_merge_FragPipe_STS26T_demonstration Jul 17, 2025 1 ❌ ✅ ❌
Neoantigen 3: PepQuery2 Verification GigaScience_PepQuery2_demonstration_STS26T_neoantigen_candidates_workflow Jul 17, 2025 1 ❌ ✅ ❌
Neoantigen 4: Variant Annotation GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates_workflow Jul 17, 2025 1 ❌ ✅ ❌
Neoantigen 5a: Predicting HLA Binding GigaScience-RNAseq-Optitype-seq2HLA-to-IEDB-alleles Jul 17, 2025 1 ❌ ✅ ❌
Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides GigaScience-IEDB-PepQuery-Neoantigen Jul 17, 2025 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 a 3D protein folding structure
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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