PTM Proteomics for Beginners: Hands-on Workshop

The Goeddel Family Technology Sandbox and Thermo Fisher Scientific are co-hosting this free, hands-on workshop designed for graduate students, postdocs, researchers and faculty in academia and industry interested in proteomics, mass spectrometry and advanced data analysis.

Join us on September 9-10 to learn about and gain practical experience with:

• The basics of proteomics, experimental planning and enrichment-based sample preparation of Post-Translational Modification (PTM) peptides by IMAC and PTMScan® methods; 
• Mass spec-based PTM quantitative proteomics using the Orbitrap Eclipse MS, including data acquisition for data-independent acquisition (DIA) or data-dependent (DDA) analysis;
• Data analysis by Thermo Fisher Scientific Proteome Discoverer pipeline and understanding secondary data analysis approaches, including pathway analysis and proteomics data reporting; and
• Quantitative proteomics MS methods on the Oribitrap Eclipse.

Workshop sessions will cover:

• Workshop introduction and overview of the Goeddel Family Technology Sandbox  
• Overview of proteomics and experimental plan, including phosphopeptides and Ubiquitin Remnant Motif (K-e-GG) enrichment sample preparation
• MS-based PTM proteomics on the Oribitrap Eclipse
• Peptide clean-up
• Peptide drying 
• Sample submission for MS-data acquisition, overview different workflows
• MS data analysis overview and Proteome Discoverer set up
• PTM mass spec data analysis by DIA or DDA approaches
• MS results reporting

Registration and Waitlist 

Registration for the full two-day workshop is now full, but don't worry! You may still be able to participate by:

• Registering for Day 2 (Data Analysis), which remains open and includes the lectures and hands-on data analysis session; and/or
• Joining the waitlist for the full two-day workshop. If a spot becomes available, waitlisted participants will be contacted in the order they joined the waitlist. Because cancellations are common, there is a good chance of receiving a spot, so we encourage you to add your name to the waitlist if you're interested in attending the full workshop.

View Workshop Agenda

 

Goeddel Family Technology Sandbox Tour

(optional, space-limited)

Tour the Goeddel Family Technology Sandbox before the workshop! A limited number of spaces will be available for workshop participants to tour the Technology Sandbox in the afternoon on Tuesday, September 8 (time TBA).

UPDATE: There is another opportunity to visit the Technology Sandbox! The UC San Diego Technology Summit 2026 on August 28th between 10:30am and 2:30pm will feature stops at the Technology Sandbox.