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:

orcid logoBérénice Batut avatar Bérénice BatutMatthias Bernt avatar Matthias BerntAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDelphine Lariviere avatar Delphine LariviereFlorence Combes avatar Florence CombesFlorian Christoph Sigloch avatar Florian Christoph Siglochorcid logoMartin Čech avatar Martin ČechDechen Bhuming avatar Dechen Bhumingorcid logoPavankumar Videm avatar Pavankumar VidemYves Vandenbrouck avatar Yves Vandenbrouckorcid logoArmin Dadras avatar Armin Dadrasorcid logoHelena Rasche avatar Helena Rascheorcid logoMelanie Föll avatar Melanie FöllNiall Beard avatar Niall BeardRay Sajulga avatar Ray Sajulgaorcid logoJayadev Joshi avatar Jayadev Joshiorcid logoClemens Blank avatar Clemens BlankDavid Christiany avatar David ChristianyValentin Loux avatar Valentin LouxKatherine Do avatar Katherine DoJames Johnson avatar James JohnsonPraveen Kumar avatar Praveen KumarKlemens Fröhlich avatar Klemens Fröhlichorcid logoKristina Gomoryova avatar Kristina Gomoryovaorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoSubina Mehta avatar Subina MehtaThorben Stehling avatar Thorben Stehlingorcid logoMatthias Fahrner avatar Matthias Fahrnerorcid logoDaniel Blankenberg avatar Daniel BlankenbergMarie Crane avatar Marie CraneEmma Leith avatar Emma Leithorcid logoBjörn Grüning avatar Björn GrüningWilliam Durand avatar William Durandorcid logoHelge Hecht avatar Helge Hechtorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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