This is the participant's page for the 2 1/2-day Proteomics 202 Short Course at MSACL on January 21 - 23, 2018 in Palm Springs, CA.

We are look forward to seeing you in Palm Springs, but before you board your flight to southern California, there are a few pieces of information we'd like to pass along and there is some preparation you need to do prior to the course. The workshop is part lecture and part hands-on tutorial, so: 

• Plan on bringing a PC laptop to the workshop. 
• • It is possible to use a Mac laptop, but takes considerably more preparation, since you will need to either set the Mac up for dual boot to Windows or a Windows VM (VMWare has been recommended for this in the past).
• Install Skyline 4.1 (the latest release) on your laptop. You can download Skyline from here: Skyline 4.1 - 64 bit or from the blue button on the Skyline website homepage.
• All other materials (aside from the laptop) will be provided after you arrive. This will include a USB flash drive with data sets that we will use in the "hands-on" sessions. If your organization/institution prohibits you from using a USB flash, please download the drive contents from this page (below).

Tutorial files

Schedule

Course Instructors

When:
Sunday, Jan 21 from 2-6pm
Monday, Jan 22 from 8-5pm (1 hr. for lunch at noon) 
Tuesday, Jan 23 from 8-noon

Where:  
All sessions are in Chino B

Additional information:
Available from the course page on the MSACL website. 

As the instructors finalize their presentations, we will post them here for future reference: 

Course Content:

Day 1

2:00 pm MacCoss - Quant Intro
3:10 pm Spencer - Proteomics Specific Considerations
4:15 pm  MacLean - Intro to Skyline
4:45 pm MacLean - Hands-on: Targeted Method Editing in Skyline

Day 2

8:00 am MacLean - Targeted Method Refinement
9:30 am Spencer - Building on Prior Knowledge
10:45 am MacLean - Hands-on: Data Analysis in Skyline
1:00 pm Pino - Calibration in Proteomics
2:00 pm MacLean - Hands-on: Calibration in Skyline
3:15 pm Pino - System Suitability and Quality Control

 Day 3

8:00 am MacCoss - Case Studies in Targeted Proteomics #1
9:00 am MacCoss - Intro to Data Independent Acquisition
10:00 am MacLean - Hands-on: DIA analysis with Skyline
11:00 am Spencer - Case Studies in Targeted Proteomics #2

Supplemental material: 

Lpino - Statistical Design

All Content in Zip file (32MB)

If you have any data you would like to discuss, please bring it with you. We will try to make time for looking at your real data.

We and all other instructors are looking forward to meeting you very soon, and engaging in a stimulating couple of days of learning and discussing targeted proteomics and ways in which Skyline can help your research.

See you all soon.

--Mike MacCoss and Brendan MacLean
Course Organizers

The following instructors and speakers have agreed to contribute their expertise to the success of the 2018 Proteomics 202 Short Course at MSACL:

		Michael J. MacCoss, Ph.D. Mike became interested in biomedical applications of mass spectrometry while working in Dr. Patrick Griffin’s protein mass spectrometry lab at Merck Research Laboratories. He obtained a Ph.D. with Professor Dwight Matthews and pursued a postdoc with Professor John R. Yates III. In 2004 he started the MacCoss lab at the University of Washington and it became obvious that while mass spectrometry data could be collected quickly and robustly, the lack of computational tools for the visualization and analysis of these data was a stumbling block. In 2009 he recruited Brendan MacLean with the goal of developing professional quality software tools for quantitative proteomics. Mike has worked closely with the Skyline development team and our outstanding group of laboratory scientists and collaborators to ensure that our software uses analytical approaches that have been thoroughly vetted by the mass spectrometry community.
		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.
		Lindsay K. Pino is a Ph.D. candidate at the University of Washington’s Department of Genome Sciences in the MacCoss lab. Her research interests include the development of large-scale proteomics assays using data independent acquisition-MS to investigate complex mixtures and applying computational techniques to mine the resulting high-dimensional data. Prior to joining the MacCoss lab, she worked as a research associate at the Broad Institute of MIT and Harvard in Dr. Steve Carr’s Proteomics Platform, where she worked under Dr. Susan Abbatiello to improve the speed and selectivity of targeted proteomics assays using high-field asymmetric waveform ion mobility spectrometry (FAIMS).
		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.