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 logoDelphine Lariviere avatar Delphine LariviereEmma Leith avatar Emma Leithorcid logoHelge Hecht avatar Helge HechtMarie Crane avatar Marie Craneorcid logoDaniel Blankenberg avatar Daniel BlankenbergJames Johnson avatar James JohnsonKatherine Do avatar Katherine Doorcid logoMelanie Föll avatar Melanie FöllDavid Christiany avatar David ChristianyWilliam Durand avatar William Durandorcid logoHelena Rasche avatar Helena Rascheorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoJayadev Joshi avatar Jayadev JoshiDechen Bhuming avatar Dechen Bhumingorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoClemens Blank avatar Clemens BlankValentin Loux avatar Valentin LouxNiall Beard avatar Niall Beardorcid logoMartin Čech avatar Martin ČechPraveen Kumar avatar Praveen Kumarorcid logoMatthias Fahrner avatar Matthias FahrnerYves Vandenbrouck avatar Yves VandenbrouckRay Sajulga avatar Ray SajulgaFlorian Christoph Sigloch avatar Florian Christoph SiglochFlorence Combes avatar Florence CombesAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSubina Mehta avatar Subina MehtaThorben Stehling avatar Thorben Stehlingorcid logoKristina Gomoryova avatar Kristina Gomoryovaorcid logoBérénice Batut avatar Bérénice BatutKlemens Fröhlich avatar Klemens Fröhlichorcid logoBjörn Grüning avatar Björn Grüningorcid logoNicola Soranzo avatar Nicola SoranzoMatthias Bernt avatar Matthias Berntorcid logoArmin Dadras avatar Armin Dadras

Funding

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