Proteomics — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

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

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
Sufficient Editorial Board Members Done ✅ (4 members) Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Done ✅ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Pending ❌ By annotating the funders of your topic's materials, you make it easier to write your grant reports later
Learning Pathway CTA Pending ❌ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.

Topic Materials

Material Contributions v2 help Pre-requisites help 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
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-normal-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 Feb 9, 2025 1
EncyclopeDIA EncyclopeDIA-GTN Feb 9, 2025 2
Label-free data analysis using MaxQuant Proteomics: MaxQuant workflow Feb 9, 2025 6
Library Generation for DIA Analysis DIA_lib_OSW Feb 9, 2025 1
MaxQuant and MSstats for the analysis of TMT data MaxQuant MSstatsTMT Training Feb 9, 2025 1
MaxQuant and MSstats for the analysis of label-free data Proteomics: MaxQuant and MSstats LFQ workflow Feb 9, 2025 3
Peptide and Protein ID using OpenMS tools Proteomics: Peptide and Protein ID using OpenMS Feb 9, 2025 6
Peptide and Protein ID using OpenMS tools Peptide And Protein ID Via OMS Using Two Search Engines Feb 9, 2025 4
Peptide and Protein ID using SearchGUI and PeptideShaker Peptide And Protein ID Tutorial Feb 9, 2025 4
Peptide and Protein ID using SearchGUI and PeptideShaker ProteinID SG PS Tutorial WF datasetCollection Feb 9, 2025 4
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) Proteomics: Peptide and Protein Quantification via stable istobe labeling Feb 9, 2025 7
Protein FASTA Database Handling Proteomics: database handling Feb 9, 2025 5
Protein FASTA Database Handling Proteomics: database handling including mycoplasma Feb 9, 2025 6
Annotating a protein list identified by LC-MS/MS experiments 'Proteome Annotation' Feb 9, 2025 3
Annotating a protein list identified by LC-MS/MS experiments ProteoRE ProteomeAnnotation Tutorial (release 2.0) Feb 9, 2025 4
Biomarker candidate identification 'Biomarkers4Paris' Workflow Feb 9, 2025 3
Secretome Prediction Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper Feb 9, 2025 3
Statistical analysis of DIA data DIA_analysis_MSstats Feb 9, 2025 2
Statistical analysis of DIA data DIA_analysis_MSstats Feb 9, 2025 2
Detection and quantitation of N-termini (degradomics) via N-TAILS Tails Triple Dimethyl OpenMS2.1 Feb 9, 2025 4
Mass spectrometry imaging: Loading and exploring MSI data MS Imaging Loading Exploring Data Feb 9, 2025 4
Metaproteomics tutorial Metaproteomics_GTN Feb 9, 2025 7
Proteogenomics 1: Database Creation GTN Proteogenomics1 Database Creation Feb 9, 2025 8
Proteogenomics 2: Database Search GTN Proteogemics2 Database Search Feb 9, 2025 7
Proteogenomics 3: Novel peptide analysis GTN Proteogemics3 Novel Peptide Analysis Feb 9, 2025 6
metaQuantome 1: Data creation metaQuantome_datacreation_workflow Feb 9, 2025 3
metaQuantome 2: Function metaquantome-function-worklow Feb 9, 2025 2
metaQuantome 3: Taxonomy metaquantome-taxonomy-workflow Feb 9, 2025 2
Machine Learning Modeling of Anticancer Peptides PeptideML Feb 9, 2025 1
Peptide Library Data Analysis Copy of PeptideDataAnalysis (imported from uploaded file) Feb 9, 2025 1
Clinical Metaproteomics 1: Database-Generation WF1_Database_Generation_Workflow Feb 9, 2025 1
Clinical Metaproteomics 2: Discovery WF2_Discovery-Workflow Feb 9, 2025 1
Clinical Metaproteomics 3: Verification WF3_VERIFICATION_WORKFLOW Feb 9, 2025 1
Clinical Metaproteomics 4: Quantitation WF4_Quantitation_Workflow Feb 9, 2025 1
Clinical Metaproteomics 5: Data Interpretation WF5_Data_Interpretation_Worklow Feb 9, 2025 1
Neoantigen 1: Fusion-Database-Generation Gigascience_Fusions_demonstration_STS26T-Gent_Workflow Feb 9, 2025 1
Neoantigen 2: Non-normal-Database-Generation Gigascience_Indels_SAV_non-normal_demonstration_STS26T-Gent_Workflow Feb 9, 2025 1
Neoantigen 3: Database merge and FragPipe discovery GigaScience_Database_merge_FragPipe_STS26T_demonstration Feb 9, 2025 1
Neoantigen 4: PepQuery2 Verification GigaScience_PepQuery2_demonstration_STS26T_neoantigen_candidates_workflow Feb 9, 2025 1
Neoantigen 5: Variant Annotation GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates_workflow Feb 9, 2025 1
Neoantigen 6: Predicting HLA Binding GigaScience-RNAseq-Optitype-seq2HLA-to-IEDB-alleles Feb 9, 2025 1
Neoantigen 7: IEDB binding PepQuery Validated Neopeptides GigaScience-IEDB-PepQuery-Neoantigen Feb 9, 2025 1

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