The African Centre for Gene Technologies (ACGT) partnered with the Council for Scientific and Industrial Research (CSIR), the University of Cape Town (UCT) and the Centre for Proteomic and Genomic Research (CPGR) to host the 2019 proteomics advanced workshop and symposium. The advanced workshop, which took place from the 18th to the 21st of November 2019, focused on the analysis of targeted proteomic and metabolomic data, using the open-source software package Skyline. The workshop was immediately followed by a national proteomics symposium, on the 22nd of November 2019, which provided emerging scientists in the field an ideal platform to showcase their work.
The four-day workshop was facilitated by Mr Brendan MacLean (MacCoss lab, University of Washington), Dr Birgit Schilling (Buck Institute for Research in Aging), Dr Ben Collins (Queen’s University Belfast and formerly Aebersold lab, ETH Zurich) and Dr Lindsay Pino (Garcia Lab, University of Pennsylvania and formerly MacCoss lab, University of Washington). The workshop had theory and practical sessions and covered a number of topics including:
- Brief introduction to targeted analysis;
- Skyline overview;
- Targeted Selected Reaction Monitoring: Method development and Data analysis;
- Targeted SWATH/ Data-Independent Acquisition: Introduction, Suitability (QC) test, library generation, data processing;
- Panaroma and AutoQC;
- Statistical group comparisons in Skyline; and
- Small molecule applications in Skyline.
The participants represented various research institutions from across the country, including the Universities of Pretoria (UP), the Witwatersrand (Wits), Johannesburg (UJ), Stellenbosch, Cape Town, the CSIR and CPGR. The participants were also given an opportunity to engage with the experts on a one-to-one basis to discuss their projects.
The symposium, which followed the workshop, had the workshop facilitators as keynote speakers as well as local researchers presenting their work. Local speakers hailed from a number of South African institutions including UP, Wits, CSIR and UCT. The symposium was a great platform to showcase what has been transpiring in the field since the last national meeting, which took place at Wits in 2018. The symposium also gave emerging scientists the opportunity to network with established researchers in the field.
Dr Ben Collins (Queen’s University Belfast) – Keynote speaker
Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage
Dr Previn Naicker (CSIR)
Development of sample preparation workflows and application to Clinical Proteomics
Mr Matthys Potgieter (UCT)
MetaNovo: a probabilistic pipeline for peptide and polymorphism discovery in complex metaproteomic datasets
Mr Brendan MacLean (University of Washington) – Keynote speaker
Growth in the software ecosystem for targeted quantitative proteomics
Dr Tracy Hurrell (CSIR)
Contextualizing the proteome of hepatocyte models
Mr Andea Ellero (UP)
Time course convergence of hepatocellular proteomic phenotypes seen in HepG2 spheroid cultures
Mr Emmanuel Nweke (Wits)
Deciphering the proteomic landscape of Pancreatic Ductal Adenocarcinoma in South African patients using SWATH mass spectrometry
Dr Birgit Schilling (Buck Institute for Research in Aging) – Keynote speaker
Proteomic tools to decipher mechanisms of senescence in aging and age-related diseases
Dr Shaun Garnett (UCT)
Generating a proteomic profile of neurogenesis, through the use of human foetal neural stem cells
Mr Daniel Mutithu (UCT)
Metabolic profiling for biomarker discovery to understand pathogenesis of rheumatic heart disease
Dr Lindsay Pino (University of Washington) – Keynote speaker
Using an external reference material to harmonize and calibrate quantitative mass
spectrometry data at scale
Establishing a community of practice for the proteomics society came up during the welcome address and closing remarks given by Prof Jonathan Blackburn from UCT and Mr Thabo Khoza from the ACGT. Mr Khoza highlighted that an informal platform (Google Groups) has been set up by the ACGT to encourage the researchers in the field to communicate more effectively. This platform is open to any researcher who wishes to join it.
The workshop and symposium would have not been possible without the generous financial support from Anatech, Bruker, Inqaba Biotec, Microsep and The Scientific Group.
The ACGT will engage with the community to plan and organise the next national proteomics workshop and national symposium for the year 2020.
For any queries related to this, or other proteomics capacity-building and networking events, contact Mr Thabo Khoza, Liaison Scientist at:
To see more photos, please visit our ACGT Facebook page.
Story by: ACGT, December 2019