proteomics

Tutorials covering proteomics

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

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
DDA human
Biomarker candidate identification
DDA human
Clinical Metaproteomics 1: Database-Generation
label-TMT11
Clinical Metaproteomics 2: Discovery
label-TMT11
Clinical Metaproteomics 3: Verification
label-TMT11
Clinical Metaproteomics 4: Quantitation
label-TMT11
Clinical Metaproteomics 5: Data Interpretation
label-TMT11
DIA Analysis using OpenSwathWorkflow
DIA
Detection and quantitation of N-termini (degradomics) via N-TAILS
EncyclopeDIA
DIA
Label-free data analysis using MaxQuant
DDA label-free
Label-free versus Labelled - How to Choose Your Quantitation Method
DDA
Library Generation for DIA Analysis
DIA
Machine Learning Modeling of Anticancer Peptides
ML cancer
Mass spectrometry imaging: Loading and exploring MSI data
mouse imaging mass spectrometry imaging
MaxQuant and MSstats for the analysis of TMT data
DDA TMT
MaxQuant and MSstats for the analysis of label-free data
label-free
Metaproteomics tutorial
microgalaxy
Multiomics data analysis using MultiGSEA
multi-omics transcriptomics proteomics metabolomics
Multiomics data analysis using MultiGSEA
multi-omics transcriptomics proteomics metabolomics
Neoantigen 1a: Fusion-Database-Generation
label-free
Neoantigen 1b: Non-Reference-Database-Generation
label-free
Neoantigen 2: Database merge and FragPipe discovery
label-free
Neoantigen 3: PepQuery2 Verification
label-free
Neoantigen 4: Variant Annotation
label-free
Neoantigen 5a: Predicting HLA Binding
label-free
Neoantigen 5b: IEDB binding Validated Neopeptides
label-free
Peptide Library Data Analysis
Peptide and Protein ID using OpenMS tools
DDA HeLa
Peptide and Protein ID using SearchGUI and PeptideShaker
DDA HeLa
Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
DDA SILAC
Protein FASTA Database Handling
DDA
Proteogenomics 1: Database Creation
proteogenomics
Proteogenomics 2: Database Search
proteogenomics
Proteogenomics 3: Novel peptide analysis
proteogenomics
Statistical analysis of DIA data
DIA
metaQuantome 1: Data creation
microgalaxy
metaQuantome 2: Function
microgalaxy
metaQuantome 3: Taxonomy
microgalaxy

Contributors

This material was contributed to by:

orcid logoCristóbal Gallardo avatar Cristóbal GallardoYves Vandenbrouck avatar Yves VandenbrouckFlorian Christoph Sigloch avatar Florian Christoph Siglochorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoWolfgang Maier avatar Wolfgang Maierorcid logoArmin Dadras avatar Armin Dadrasorcid logoMartin Čech avatar Martin Čechorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLucille Delisle avatar Lucille DelisleWilliam Durand avatar William Durandorcid logoBjörn Grüning avatar Björn Grüningorcid logoTimothy J. Griffin avatar Timothy J. Griffinorcid logoMatthias Fahrner avatar Matthias FahrnerDechen Bhuming avatar Dechen Bhumingorcid logoNicola Soranzo avatar Nicola SoranzoValentin Loux avatar Valentin Louxorcid logoMatthias Bernt avatar Matthias BerntEmma Leith avatar Emma LeithKatherine Do avatar Katherine Doorcid logoMallory Freeberg avatar Mallory FreebergMélanie Pétéra avatar Mélanie Pétéraorcid logoMelanie Föll avatar Melanie FöllJames Johnson avatar James JohnsonAnton Nekrutenko avatar Anton NekrutenkoPraveen Kumar avatar Praveen KumarMarie Crane avatar Marie Craneorcid logoClemens Blank avatar Clemens Blankorcid logoHelge Hecht avatar Helge HechtThorben Stehling avatar Thorben StehlingDavid Christiany avatar David Christianyorcid logoSubina Mehta avatar Subina Mehtaorcid logoBérénice Batut avatar Bérénice Batutorcid logoDaniel Blankenberg avatar Daniel BlankenbergKlemens Fröhlich avatar Klemens Fröhlichorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoJayadev Joshi avatar Jayadev Joshiorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena RascheRay Sajulga avatar Ray SajulgaFlorence Combes avatar Florence Combesorcid logoKristina Gomoryova avatar Kristina GomoryovaNiall Beard avatar Niall Beard

Funding

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

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UFR
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de.NBI
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ELIXIR Europe