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
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