proteomics

Tutorials covering proteomics

Material

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Proteomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Annotating a protein list identified by LC-MS/MS experiments
Biomarker candidate identification
Clinical Metaproteomics 1: Database-Generation
Clinical Metaproteomics 2: Discovery
Clinical Metaproteomics 3: Verification
Clinical Metaproteomics 4: Quantitation
Clinical Metaproteomics 5: Data Interpretation
DIA Analysis using OpenSwathWorkflow
DIA
Detection and quantitation of N-termini (degradomics) via N-TAILS
EncyclopeDIA
DIA
Introduction to proteomics, protein identification, quantification and statistical modelling
Label-free data analysis using MaxQuant
Label-free versus Labelled - How to Choose Your Quantitation Method
DDA
Library Generation for DIA Analysis
DIA
Machine Learning Modeling of Anticancer Peptides
Mass spectrometry imaging: Loading and exploring MSI data
MaxQuant and MSstats for the analysis of TMT data
MaxQuant and MSstats for the analysis of label-free data
Metaproteomics tutorial
Multiomics data analysis using MultiGSEA
Multiomics data analysis using MultiGSEA
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
Peptide Library Data Analysis
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
DDA
Proteogenomics 1: Database Creation
Proteogenomics 2: Database Search
Proteogenomics 3: Novel peptide analysis
Single Cell Proteomics data analysis with bioconductor-scp
Statistical analysis of DIA data
DIA
metaQuantome 1: Data creation
metaQuantome 2: Function
metaQuantome 3: Taxonomy

Contributors

This material was contributed to by:

Florian Christoph Sigloch avatar Florian Christoph Siglochorcid logoMatthias Fahrner avatar Matthias Fahrnerorcid logoKristina Gomoryova avatar Kristina Gomoryovaorcid logoMartin Čech avatar Martin ČechKatherine Do avatar Katherine DoDavid Christiany avatar David Christianyorcid logoClemens Blank avatar Clemens BlankThorben Stehling avatar Thorben StehlingPraveen Kumar avatar Praveen KumarYves Vandenbrouck avatar Yves Vandenbrouckorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBérénice Batut avatar Bérénice BatutEmma Leith avatar Emma LeithNiall Beard avatar Niall Beardorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMelanie Föll avatar Melanie FöllMatthias Bernt avatar Matthias Berntorcid logoSubina Mehta avatar Subina Mehtaorcid logoTimothy J. Griffin avatar Timothy J. GriffinWilliam Durand avatar William Durandorcid logoArmin Dadras avatar Armin Dadrasorcid logoJayadev Joshi avatar Jayadev Joshiorcid logoPratik Jagtap avatar Pratik JagtapAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDaniel Blankenberg avatar Daniel BlankenbergValentin Loux avatar Valentin Louxorcid logoHelge Hecht avatar Helge HechtMarie Crane avatar Marie Craneorcid logoBjörn Grüning avatar Björn GrüningRay Sajulga avatar Ray Sajulgaorcid logoDelphine Lariviere avatar Delphine LariviereDechen Bhuming avatar Dechen BhumingJames Johnson avatar James JohnsonFlorence Combes avatar Florence Combesorcid logoHelena Rasche avatar Helena RascheKlemens Fröhlich avatar Klemens Fröhlich

Funding

These individuals or organisations provided funding support for the development of this resource