proteomics

Tutorials covering proteomics

Material

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Proteomics

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to proteomics, protein identification, quantification and statistical modelling
Single Cell Proteomics data analysis with bioconductor-scp
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
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
Statistical analysis of DIA data
DIA
metaQuantome 1: Data creation
metaQuantome 2: Function
metaQuantome 3: Taxonomy

Contributors

This material was contributed to by:

Emma Leith avatar Emma LeithAnton Nekrutenko avatar Anton NekrutenkoJames Johnson avatar James Johnsonorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoHelena Rasche avatar Helena RascheDechen Bhuming avatar Dechen BhumingDavid Christiany avatar David Christianyorcid logoMatthias Bernt avatar Matthias Berntorcid logoSubina Mehta avatar Subina Mehtaorcid logoBjörn Grüning avatar Björn Grüningorcid logoArmin Dadras avatar Armin Dadrasorcid logoHelge Hecht avatar Helge HechtThorben Stehling avatar Thorben StehlingRay Sajulga avatar Ray SajulgaKlemens Fröhlich avatar Klemens Fröhlichorcid logoKristina Gomoryova avatar Kristina Gomoryovaorcid logoTimothy J. Griffin avatar Timothy J. GriffinNiall Beard avatar Niall Beardorcid logoBérénice Batut avatar Bérénice Batutorcid logoMelanie Föll avatar Melanie FöllYves Vandenbrouck avatar Yves Vandenbrouckorcid logoDaniel Blankenberg avatar Daniel BlankenbergFlorence Combes avatar Florence Combesorcid logoPratik Jagtap avatar Pratik JagtapWilliam Durand avatar William Durandorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoDelphine Lariviere avatar Delphine LariviereFlorian Christoph Sigloch avatar Florian Christoph Siglochorcid logoJayadev Joshi avatar Jayadev Joshiorcid logoMartin Čech avatar Martin ČechPraveen Kumar avatar Praveen KumarMarie Crane avatar Marie Craneorcid logoClemens Blank avatar Clemens BlankKatherine Do avatar Katherine DoValentin Loux avatar Valentin Louxorcid logoMatthias Fahrner avatar Matthias Fahrnerorcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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