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 logoNicola Soranzo avatar Nicola SoranzoKlemens Fröhlich avatar Klemens FröhlichRay Sajulga avatar Ray SajulgaDechen Bhuming avatar Dechen Bhumingorcid logoSubina Mehta avatar Subina Mehtaorcid logoDelphine Lariviere avatar Delphine LariviereValentin Loux avatar Valentin LouxEmma Leith avatar Emma LeithMatthias Bernt avatar Matthias Berntorcid logoSaskia Hiltemann avatar Saskia HiltemannMarie Crane avatar Marie CraneThorben Stehling avatar Thorben StehlingYves Vandenbrouck avatar Yves VandenbrouckKatherine Do avatar Katherine DoFlorence Combes avatar Florence Combesorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn GrüningNiall Beard avatar Niall BeardPraveen Kumar avatar Praveen Kumarorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoHelge Hecht avatar Helge Hechtorcid logoMatthias Fahrner avatar Matthias Fahrnerorcid logoArmin Dadras avatar Armin DadrasDavid Christiany avatar David Christianyorcid logoMartin Čech avatar Martin Čechorcid logoHelena Rasche avatar Helena RascheWilliam Durand avatar William Durandorcid logoJayadev Joshi avatar Jayadev Joshiorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoClemens Blank avatar Clemens BlankAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoKristina Gomoryova avatar Kristina Gomoryovaorcid logoPavankumar Videm avatar Pavankumar VidemJames Johnson avatar James Johnsonorcid logoMelanie Föll avatar Melanie FöllFlorian Christoph Sigloch avatar Florian Christoph Sigloch

Funding

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