Proteomics — Editorial Board Home

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Editorial Board

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

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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 1: Fusion-Database-Generation ✅ ✅ ✅ ✅
Neoantigen 2: Non-Reference-Database-Generation ✅ ✅ ✅ ✅
Neoantigen 3: Database merge and FragPipe discovery ✅ ✅ ✅ ✅
Neoantigen 4: PepQuery2 Verification ✅ ✅ ✅ ✅
Neoantigen 5: Variant Annotation ✅ ✅ ✅ ✅
Neoantigen 6: Predicting HLA Binding ✅ ✅ ✅ ✅
Neoantigen 7: IEDB binding PepQuery Validated Neopeptides ✅ ✅ ✅

Topic Workflows

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