Mass spectrometry-based Proteomics introduction#

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.

Location#

Room 011/ALC2 in building 208 at DTU.

Agenda#

Time	Topic	lecturer
09.00 - 09:10	Welcome, coffee, and setup	-
09:10 - 11.00	Introduction with overview of all the components	Marco Reverenna
11.00 - 11.15	break	-
11.15 - 12.15	Steps in data processing and running quantms hands-on	Henry Webel
12.15 - 13.00	Lunch (sandwiches are provided)	-
13.00 - 14.30	Steps in statistical analysis (lecture )	Alberto Santos
14.30 - 15.00	break	-
15.00 - 16.30	Steps in statistical analysis (Hands-On)	Henry Webel

Each 90mins session will have a small break of 5mins inbetween.

Some details to the agenda points#

09.10 - 11.00 - Introduction#

See the slides for introduction here.

11.15 - 12.15 - data processing and hands-on quantms#

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

13.00 - 14.30 - statistical analysis lecture#

See the slides for the statistical analysis here.

15.00 - 16.30 - hands-on statistical analysis#