Pre-Lorne Workshop

Pre-Lorne Workshop

29-31 January 2018, University of Melbourne

Targeted Proteomics Strategies – Skyline, DDA and DIA/SWATH

This Pre-Lorne Workshop sponsored by SCIEX and the Australasian Proteomics Society will introduce theoretical and practical concepts in targeted proteomics. Topics that will be covered include targeted acquisition focusing on selected reaction monitoring (SRM), data dependent acquisition strategies, statistical considerations, label-free quantitation and data independent acquisition (DIA) mass spectrometry (including SWATH-MS). We will introduce the targeted proteomic software environment Skyline and provide hands-on tutorials that demonstrate its functionality for the analysis of SRM, DDA and DIA/SWATH-MS data. Participants will be required to bring their own laptop with Skyline installed (requires Windows, or a Windows virtual machine for Mac/Linux users). Some basic knowledge of mass spectrometry-based proteomics is assumed. 

Brendan MacLean – University of Washington
Sandi Spencer – University of Washington
Brian Searle – Proteome Software / University of Washington

Closing Keynote Lecture:
Professor Ruedi Aebersold – ETH Zurich

Registration: $175; Students: $100 - click here for more details on registration

The Pre-Lorne Workshop is proudly sponsored by


Register for the Pre-Lorne Workshops via the 23rd Annual Lorne Proteomics Symposium portal: 

Accommodation has been arranged at the Rydges on Swanston at the special delegate rates. Please click the tab below for more details.


(Preliminary Program - Subject to changes)

Monday 29th January




10:30 - 10:40 Brendan MacLean Opening Remarks
10:40 - 11:40  Sandi Spencer Lecture: Moving from discovery to targeted Proteomics 
11:40 - 12:40  Brendan MacLean Lecture: Introduction to Skyline 
12:40 - 1:30  Lunch
1:30 - 2:45  Brendan MacLean Hands-on: Targeted method editing in Skyline 
2:45 - 4:00  Brendan MacLean Hands-on: Targeted method refinement in Skyline 
4:00 - 4:30  Break
4:30 - 5:30  Sandi Spencer Lecture: Building prior knowledge for SRM assays 









Tuesday 30th January

Time Speaker Topic
8:30 - 9:45  Brendan MacLean Hands-on: Data analysis in Skyline 
9:45 - 10:45  Sandi Spencer Lecture: Protein quantification 
10:45 - 11:15        Break
11:15 - 12:15        Brendan MacLean    Hands-on: Calibrated quantification with Skyline 
12:15 - 1:15  Brendan MacLean Hands-on: Group comparison statistics and reports in Skyline 
1:15 - 2:00  Lunch
2:00 - 2:30  Brendan MacLean

Lecture: Overview and keys to success in processing DDA data with Skyline 

2:30 - 4:00  Brendan MacLean Hands-on: Label-free quantitative analysis of DDA data with Skyline 
4:00 - 4:30  Break
4:30 - 6:00  Sandi Spencer Hands-on: Parallel reaction monitoring (PRM) with Skyline 














Wednesday 31st January

Time Speaker Topic
9:00 - 10:00  Brian Searle Lecture: Data independent acquisition 
10:00 - 10:30  Break
10:30 - 12:30    Tutorial: DIA data analysis with Skyline (ETH tutorial)
12:30 - 1:30  Lunch
1:30 - 3:30  Brian Searle Hands-on: Data independent acquisition data analysis 
3:30 - 4:00  Break
4:00 - 5:00  Ruedi Aebersold Keynote: Targeting proteomics at high throughput