The course will introduce MS-based proteomics data, it's basic processing and the downstream analysis. The course will be a mix of lectures and hands-on session where we will perform the basic processing steps using quantms, a nextflow workflow, and acore, short for analytical core for the downstream analysis.
| Time | Topic | lecturer |
|---|---|---|
| 8.30 - 10.00 | Introduction with overview of all the components | Marco Reverenna |
| 10.30 - 12.00 | Steps in data processing and running quantms hands-on | Henry Webel |
| 12.00 - 13.00 | Lunch (sandwiches are provided) | - |
| 13.00 - 14.30 | Steps in statistical analysis (lecture ) | Alberto Santos |
| 15.00 - 16.30 | Steps in statistical analysis (Hands-On) | Henry Webel |
See the slides for introduction here.
Find the instruction here and the slides here
Steps in data processing (using quantms)
- FASTA file to define search space
- Spectrum files from Mass-spectrometer
- Running quantms to process spectra to identified and quantified peptide sequences
See the slides for the statistical analysis here.
Find the instruction here and the slides here
Basic statistical analysis of a two-group experiment with one timepoint (option 1) or four timepoints (option 2)
- Peptide to protein (group) aggregation
- Downstream data analysis of proteins (using analytical core library developed at biosustain and other Python libraries)
- Building a report with vuegen reports (developed at biosustain)
- see the documentation for an overview: docs.quantms.org
- ask question on the nf-core slack channel
quantms: https://nf-co.re/join/slack - submit an issue on the GitHub repository