Educator:
David L. Tabb (CIBI)
Date:
December 17, 2025 9:00 AM-noon
Location:
University of Antwerp
Contents:
This course teaches the use of FragPipe and FragPipe Analyst to identify and quantify DDA and DIA proteomes, seeking differential protein expression.
Proteomics technologies such as LC-MS/MS (liquid chromatography coupled with tandem mass spectrometry) are a natural fit for clinical biology because these technologies powerfully detect changes in protein concentration and modification. This hands-on training will introduce the key steps required to quantify and differentiate proteins, matching tandem mass spectra to potential peptide sequences and inferring proteins from them, integrating chromatograms to estimate quantities for peptides and proteins, and statistically testing for differences in protein quantities between two cohorts.
This study will use data from PXD044981 (https://doi.org/10.1021/acs.jproteome.4c00048), which applied both DDA (the classic LC-MS/MS identification technique) and DIA (a method intended to quantify thousands of peptides at once) to measure a yeast background with human proteins spiked at different quantities. Dr. Tabb will guide the participants through the process of identifying and quantifying these data sets in FragPipe (https://fragpipe.nesvilab.org/), followed by statistics and visualization in the FragPipe Analyst web interface.
Learning goals:
Participants should gain the ability to use the LFQ-MBR (label-free quantitation, match-between-runs) and DIA_SpecLib_Quant workflows in FragPipe 23.1. They will be able to pass the results of these analyses to the FragPipe Analyst website for detecting differential protein expression.
Prerequisites:
Participants should bring laptops to be able to carry out this training on their own computers; for best results, we suggest that the computers feature at least 8GB of RAM. FragPipe can be used in Microsoft Windows and Linux. Prior to the training, we recommend that students try to install FragPipe on their laptops in case they need administrator passwords for this process.
Keywords:
Proteomics, Bioinformatics, LC-MS/MS, MSFragger, FragPipe, biomarkers
Tools:
FragPipe, MSFragger, FragPipe Analyst
Contact:
Wout Bittremieux: