Mass spectrometry-based Proteomics introduction

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.

Agenda#

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

Some details to the agenda points#

8.30-10.00 - introduction#

See the slides for introduction here.

10.30-12.00 - 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#

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)

QuantMS help#

Contents