This is the participant's page for the 3-day Targeted Proteomics Strategies Workshop which was held prior to the 2018 Lorne Proteomics Symposium ,  January 29 - 31, 2018 in at the University of Melbourne, Parkville, VIC, Australia. 

Schedule

Course Instructors

When:
Monday, Jan 29 from 9:30-5:30pm (50 min. for lunch at 12:40pm) 
Tuesday, Jan 30 from 8:30-6pm (45 min. for lunch at 1:50pm) 
Wednesday, Jan 31 from 9-5pm (1 hr. for lunch at 12:30)

Where:  
University of Melbourne
Arts West | North Wing Building (building 148) | Lectorial Room II (Room 556 - Level 5)
Royal Parade
Parkville, VIC 3052 (Transportion options and maps)

Additional information:
Available from the Pre-Lorne Workshop course page.

Course Content:

All Presentations in zip file

Pre-Lorne Flashdrive content (5.9GB)

SWATH Tutorial Data (7.8GB)

MSstats  Addendum - slides and data

The instructors have finalized their presentations and are posted below (Hands-on sessions had no slide presentations unless otherwise noted): 

Day 1

9:30 am Registration open and morning tea
10:00 am MacLean - Opening Remarks
10:40 am Spencer - Moving from Discovery to Targeted Proteomics
11:40 am MacLean - Lecture: Introduction to Skyline
12:40 pm - Lunch
1:30 pm MacLean - Hands-on: Targeted Method Editing
2:45 pm MacLean - Lecture: Targeted Method Refinement
4:00 pm - Break
4:30 pm Spencer - Lecture: Building Prior Knowledge for SRM Assays

Day 2
8:30 am MacLean - Hands-on: Data Analysis in Skyline
9:45 am Spencer - Lecture: Protein Quantification
10:45 am - Break
11:15 am MacLean - Hands-on: Group Comparison Statistics and Reports in Skyline
12:15 pm MacLean - Hands-on: Calibrated Quantification with Skyline
1:15 pm - Lunch
2:00 pm MacLean - Lecture: Overview and Keys to Success in Processing DDA data with Skyline
2:30 pm MacLean - Hands-on: Label-free Quantitative Analysis of DDA data with Skyline
4:00 pm - Break
4:30 pm Spencer - Hands-on: Parallel Reaction Monitoring (PRM) with Skyline

Day 3
9:00 am Searle - Lecture: Introduction to DIA
9:30 am Searle - Hands-on: Extracting Peptides from DIA in Skyline
10:30 am - Break
11:00 am Searle - Lecture: Details of DIA Acquisition
11:30 am Searle - Hands-on: Large-scale DIA with DDA Libraries in Skyline
12:30 pm - Lunch
1:30 pm Searle - Hands on: Analyzing DIA with Walnut/Skyline - Instructions
3:30 pm - Break
4:00 pm Aebersold - Design and Biological Relevance of Targeted Proteomic Experiments

-- Brendan MacLean
Course Organizer

The following instructors and speakers have agreed to contribute their expertise to the success of the 2018 Pre-Lorne Workshop at the University of Melbourne:

		Brendan MacLean Brendan worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual C++/Developer Studio Project. Since leaving Microsoft, Brendan has been the Vice President of Engineering for Westside Corporation, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LakKey Software. In this last position he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline. Since August, 2008 he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community.
		Ruedi Aebersold, Ph.D. Ruedi is professor at ETH Zurich. His research has focused on the development of new technologies for quantitative proteomics and on applying them to challenging questions of contemporary life science research. In this area, the group has a worldwide standing and has pioneered a number of concepts and technologies that have transformed proteomics. These include the introduction of relative and absolute proteome quantification, the development of open source computational tools for the objective, statistically supported analysis of large proteomic datasets, the development of a method for the determination of the spatial organization of protein complexes and the development of targeted proteomic techniques such as Selected Reaction Monitoring and SWATH-MS.The concept of targeted proteomics has been selected Method of the Year 2012 by the journal Nature Methods.
		Brian Searle Brian Searle is the co-founder and chairman of the board of Proteome Software, Incorporated. Following an undergraduate degree in chemistry from Reed College, Brian was mentored in MS/MS-based proteomics by Ashley McCormack and software development by Mark Turner in Srinivasa Nagalla’s lab at Oregon Health and Science University. In 2004 Brian co-founded Proteome Software with Mark and Ashley to produce and distribute cutting-edge data analysis software for proteomicists. As the owner of Proteome Software, Brian has produced numerous innovations in the analysis of MS/MS-based proteomics data. Brian is a member of the American Society for Mass Spectrometry (ASMS) and served on the board of directors for that organization. Brian also co-founded the Proteome Informatics Research Group of the Association of Biomolecular Resource Facilities (ABRF) society and is active in ABRF committees. In addition to furthering the goals of Proteome Software, Brian is concurrently pursuing a PhD at University of Washington.
		Sandi Spencer, Ph.D. Sandi is currently a postdoctoral researcher in the MacCoss lab at the University of Washington working on method development for targeted proteomics and improvement of nanoLC robustness. She earned her Ph.D. from the University of North Carolina at Chapel Hill working in the Glish lab on real-time analysis of compounds in organic aerosol particles.