Event Date
Hands-on
Proteomics
Short Course
A week-long, openly enrolled, hands-on proteomics course — now in its 18th consecutive year at UC Davis.
Hosted on UC Davis Conferences & Events · opens in a new tab
Everything, all in one week.
The full proteomics workflow — theory, wet-lab sample prep, LC-MS/MS acquisition, and modern data analysis — taught by core staff on state-of-the-art Thermo and Bruker instruments.
Intermediate
The full proteomics workflow — all in one week.
Participants learn every stage of a modern proteomics experiment: the underlying theory, wet-lab sample preparation, LC-MS/MS acquisition on state-of-the-art mass spectrometers, and hands-on computational data analysis. It is one of very few week-long, openly enrolled proteomics courses that covers the full workflow — theory, wet-lab prep, LC-MS acquisition on multiple instrument vendors (Thermo and Bruker), and modern DIA analysis — all under one roof, with no vendor lock-in.
Run continuously since 2008 by the UC Davis Proteomics Core Facility, the course is taught by Core staff scientists with invited guest lecturers each year. Past guest lecturers have come from Stanford, UCSF, the Buck Institute, Thermo Fisher, and Bruker. The course draws participants from academia, national labs, industry, and international institutions. We start from first principles and build to modern quantitative DIA workflows by the end of the week.
Five days, one workflow, six modules.
Each module pairs short theory blocks with hands-on practice — from sample in hand to quantitative biological interpretation.
Fundamentals
What a mass spectrometer actually measures, and how those measurements become a list of proteins.
- Mass spectrometry and proteomics first principles
- Bottom-up proteomics (digesting proteins into peptides, then identifying the peptides) end-to-end
- Instrument types and when to use each
Sample Preparation
Getting proteins out of cells, tissue, or fluid — and into peptides clean enough for the mass spec to read.
- Lysis, reduction, alkylation, and digestion (the basic steps that turn a protein sample into mass-spec-ready peptides)
- Modern prep techniques: magnetic-bead digestion, S-Trap, and in-solution workflows
- Peptide cleanup and quantification
- Common pitfalls and QC checkpoints
LC-MS/MS Acquisition
How peptides get separated by liquid chromatography (LC) and measured on the mass spectrometer (MS/MS).
- Nano-scale HPLC setup and troubleshooting
- Running the two dominant modern instrument families: Orbitrap (Thermo) and timsTOF (Bruker)
- Choosing between DDA (data-dependent) and DIA (data-independent) acquisition — and why DIA is the modern default
Quantitative Analysis
How we actually count proteins across samples — the core of any comparative proteomics experiment.
- Data-Independent Analysis (DIA) workflows — the modern way to quantify thousands of proteins reproducibly across many samples
- Peptide-spectrum matching and FDR (false discovery rate) control — deciding which protein IDs to trust
- Label-free and TMT (Tandem Mass Tag) quantitation — chemical barcodes that let you multiplex many samples in a single run
Data Analysis
Turning raw mass-spec files into protein lists, quantitative tables, and biological answers.
- Hands-on with the three most widely used proteomics software tools: FragPipe and DIA-NN (free, open-source) and Spectronaut (commercial, Biognosys)
- Using AI-assisted and custom proteomics pipelines
- Statistical interpretation and visualization
- Reproducible reporting of proteomics results
Instrument Tours
Time at the bench with the two dominant classes of modern proteomics mass spectrometers.
- Bruker timsTOF HT walkthroughs (trapped-ion-mobility time-of-flight)
- Thermo Orbitrap Eclipse and Exploris series
- Past guest lectures have included scientists from Thermo Fisher and Bruker
The people teaching the course.
UC Davis Proteomics Core staff scientists — a combined 50+ years of mass spectrometry experience across academic, industry, and international proteomics labs.
Director since 2005 with two decades of mass spectrometry expertise. PI on the Core’s S10 instrument grants. Previously directed the proteomics facility at Michigan State University. Active in educational outreach through tutorials and podcasts, with a YouTube channel viewed tens of thousands of times by proteomics learners worldwide.
Two decades of hands-on LC-MS/MS experience at the UC Davis Genome Center, with a publication record spanning autophagy and cell biology, forensic and paleoproteomics, cancer biomarkers, and agricultural proteomics. Co-author on 100+ publications (h-index 34; 3,000+ citations), including a core method paper benchmarking peptide-centric DIA on Thermo Orbitrap Lumos and diaPASEF on Bruker timsTOF — the same workflows participants learn during the course. Teaches the short course annually and leads sample-preparation instruction.
Ph.D. from UC Davis in FT-ICR mass spectrometry. Former applied scientist at Thermo Fisher and former manager of proteomics at the European Institute of Oncology in Milan. Focus: Orbitrap and triple-quadrupole method development, and modern sample-prep optimization (S-Trap, SP3).
Specialist in high-throughput automated sample preparation using robotic platforms (KingFisher systems). Leads the Core’s magnetic-bead digestion workflow optimization and streamlines day-to-day sample-prep operations for hundreds of submissions per year.
Plus invited guest lecturers each year. Past guest lecturers have come from Stanford, UCSF, the Buck Institute, Thermo Fisher, and Bruker.
Verbatim from a handwritten thank-you card.
Unsolicited messages presented to instructors at the close of a recent course — signed by over a dozen researchers spanning graduate students, postdocs, and industry scientists.
Thank you all for a wonderful course that has changed my view on proteomics. I see it as my future now!
Thank you so much for organizing this amazing workshop and sharing your endless knowledge with us! I love proteomics now!
Thank you for all of the effort you guys put on this course! I enjoyed all the lectures and the tour of the instruments and will sure make use of them in the future!
Thank you! The course was great and just what I needed. Really excited to have a handle on proteomics to use for my research. You make everything so lovely.
A diverse cohort, a full week of science.
Participants from UC Davis, external academic institutions, industry, and international research labs.
Photos from the 2025 Introductory Hands-on Proteomics Short Course.
Three straightforward tiers.
No price increase this year. UC Davis trainees may additionally be eligible for full-tuition vouchers — see below.
All UC campus attendees — students, postdocs, staff, and faculty.
External academic, national labs, and international attendees.
Biotech, pharma, diagnostics, and instrument-vendor attendees.
Possible UC Davis tuition vouchers: pending the outcome of a grant submission, a limited number of full-tuition vouchers may be available for UC Davis graduate students and postdoctoral researchers. Funding is not yet confirmed — email Jeanette Martins to join the voucher waitlist (separate from course registration) and we will notify you the moment eligibility is announced. Course registration via the Register Now button above is open regardless of voucher status.
Registration is live on the UC Davis Conferences & Events platform — use any Register Now button above. W-9 and invoicing available on request. For advance quotes for PO planning, contact Jeanette Martins ([email protected]).
What to expect, practically.
Who Should Attend
- Graduate students and postdocs new to proteomics
- Staff scientists adding MS to an existing workflow
- Industry researchers moving into protein analytics
- PIs evaluating whether to adopt proteomics
What’s Provided
- All course materials and reagents
- Training samples (own samples possible with prior approval)
- Desktop computers (Windows) for analysis sessions
- Personal laptops welcome
Lodging & Meals
- UC Davis summer housing available on campus
- Meal plans bookable through campus summer housing
- Downtown Davis hotels a short bike or shuttle ride
- Daily morning coffee and snacks provided
What to Expect
- Full days — 8:00 AM to 4:00 PM
- Small cohort, high staff-to-participant ratio
- Fills by mid-July — register early
- Certificate of completion issued at course close
Ready for August 3–7, 2026?
Seats are limited and historically fill by mid-July. UC Davis graduate students and postdoctoral researchers are strongly encouraged to apply.
Registration & Logistics
Jeanette Martins, Course Coordinator
[email protected]
Scientific & Technical
[email protected]
(530) 754-9474