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 FahrnerDavid Christiany avatar David ChristianyKatherine Do avatar Katherine Doorcid logoArmin Dadras avatar Armin Dadrasorcid logoHelena Rasche avatar Helena Rascheorcid logoKristina Gomoryova avatar Kristina GomoryovaWilliam Durand avatar William Durandorcid logoMartin Čech avatar Martin Čechorcid logoTimothy J. Griffin avatar Timothy J. GriffinDechen Bhuming avatar Dechen BhumingValentin Loux avatar Valentin Louxorcid logoJayadev Joshi avatar Jayadev JoshiEmma Leith avatar Emma LeithRay Sajulga avatar Ray Sajulgaorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoMelanie Föll avatar Melanie Föllorcid logoBjörn Grüning avatar Björn GrüningYves Vandenbrouck avatar Yves Vandenbrouckorcid logoPavankumar Videm avatar Pavankumar VidemPraveen Kumar avatar Praveen Kumarorcid logoHelge Hecht avatar Helge HechtMatthias Bernt avatar Matthias BerntNiall Beard avatar Niall Beardorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBérénice Batut avatar Bérénice BatutKlemens Fröhlich avatar Klemens FröhlichThorben Stehling avatar Thorben StehlingFlorence Combes avatar Florence CombesAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSubina Mehta avatar Subina Mehtaorcid logoSaskia Hiltemann avatar Saskia HiltemannJames Johnson avatar James Johnsonorcid logoClemens Blank avatar Clemens BlankMarie Crane avatar Marie Crane

Funding

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