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:

Praveen Kumar avatar Praveen Kumarorcid logoJayadev Joshi avatar Jayadev JoshiAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMatthias Fahrner avatar Matthias FahrnerThorben Stehling avatar Thorben Stehlingorcid logoSubina Mehta avatar Subina Mehtaorcid logoArmin Dadras avatar Armin Dadrasorcid logoBérénice Batut avatar Bérénice BatutDechen Bhuming avatar Dechen Bhumingorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoBjörn Grüning avatar Björn Grüningorcid logoKristina Gomoryova avatar Kristina Gomoryovaorcid logoDelphine Lariviere avatar Delphine LariviereKatherine Do avatar Katherine Doorcid logoMartin Čech avatar Martin ČechMatthias Bernt avatar Matthias Berntorcid logoClemens Blank avatar Clemens BlankValentin Loux avatar Valentin Louxorcid logoSaskia Hiltemann avatar Saskia HiltemannFlorence Combes avatar Florence CombesJames Johnson avatar James JohnsonNiall Beard avatar Niall Beardorcid logoTimothy J. Griffin avatar Timothy J. GriffinWilliam Durand avatar William Durandorcid logoHelge Hecht avatar Helge HechtRay Sajulga avatar Ray Sajulgaorcid logoNicola Soranzo avatar Nicola SoranzoEmma Leith avatar Emma LeithDavid Christiany avatar David Christianyorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoPavankumar Videm avatar Pavankumar Videmorcid logoMelanie Föll avatar Melanie FöllFlorian Christoph Sigloch avatar Florian Christoph SiglochMarie Crane avatar Marie Craneorcid logoHelena Rasche avatar Helena RascheKlemens Fröhlich avatar Klemens FröhlichYves Vandenbrouck avatar Yves Vandenbrouck

Funding

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