Stanford University Mass Spectrometry

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Welcome to the Vincent Coates Foundation Mass Spectrometry Laboratory.

The laboratory is named in honor of a generous gift from Vincent and Stella Coates, given through the Stanford School of Medicine to support the mass spec & proteomics facility as a shared core resource. It is a Bio-X core facility, embodying the Bio-X spirit of interdisciplinary communication and collaboration. It is also partially supported as the Proteomics Shared Resource of the Stanford Cancer Institute. The Dean of Research provides oversight and support to keep the laboratory's expertise and support available to researchers throughout Stanford University & Medical Center.

 

Overview of Services

Beyond making available state-of-the-art, user-friendly facilities and services, the laboratory enables education, methods development, and new applications development, designed to meet the rapidly evolving needs of researchers. Due to the essential information that mass spectrometry provides to researchers in the fields of the physical and life sciences, medicine, and engineering, the laboratory serves as an “intellectual watering hole” at the crossroads of diverse disciplines.

At this time, we have 16 instruments in operation: three GC-MS and twelve LC-MS systems -- four single quads, one ion trap, four triple quads, one hybrid quadrupole-time of flight, one Orbitrap (Exactive), one Q-Exactive, two hybrid LTQ-Orbitraps and a Orbitrap Fusion -- as well as a MALDI-TOF. Software resources include instrument-specific packages Xcalibur, MassLynx, ChemStation; proteomics software Byonic, Mascot, Sequest Sorcerer, Scaffold; and other tools including LCquan, QuanLynx, OpenLynx, MetaboLynx, ChemStation, Mass Hunter, Spectral Works.

Routine mass spec and proteomic services include molecular weight determination from small molecules to intact proteins, high resolution MS, bottom-up proteomics and more. Please contact SUMS to discuss custom work such as complex proteomic analysis, relative and targeted quantitation, drug discovery support, de novo peptide sequencing, new application development, and other projects.

Types of Service and Analysis Offered by SUMS:

• Proteomics
• Protein identification - gel or solution based
• Shotgun proteomics, e.g. cell lysates, tissue preps
• Analysis of frozen or FFPE banked tissues
• Post-translational modification studies, e.g. phosphorylation, methylation, ubiquitination
• Quantitative studies - labeled and unlabeled differential expression; targeted absolute quantitation
• Protein interactions - SNAP, crosslinking

• Small Molecules
• Molecular weight confirmation
• High resolution molecular formula confirmation (HRMS)
• Structural elucidation (MSn)
• Targeted quantitation
• Protein characterization - intact mass, ADCs (yes, even though these aren't small)

• Drug Discovery Support
• Pharmacokinetic (PK) assessment
• Microsome incubations
• Metabolite identification
• Stability assessment
• Formulation assessment
• Degradation studies

• Assays & Quantitation
• For small molecules and proteins/peptides
• Pre-established assays for select classes of molecules
• Custom assay development for molecules or metabolic pathways of interest

• Metabolomics
• Targeted, Quantitative
• Semi-Quantitative

• Open access (Stanford Users Only)
• LC/MS
• GC/MS
• MALDI-TOF
• High res LC/MS

• Other custom projects - contact SUMS to discuss

 

Getting Started

• Stanford Users:  LOGIN with valid Stanford credentials (SUNet ID).

• Non-Stanford Users:  LOGIN using iLab credentials. Or, click to SIGN UP for an iLab account.

Leadership

Allis Chien, PhD | SUMS Director

Office (Bass 026):  (650) 723-0710

Email:  allis at stanford.edu

 

Ryan Leib, PhD | SUMS Director of Proteomics

Office (Bass 024):  (650) 725-9769

Email:  allis at stanford.edu

 

Financial Contact

William Lee | Accounting Associate

Office (Bass 024):  (650) 725-9769

Email:  wlee2 at stanford.edu

 

Staff

 

Name		Role		Phone		Email		Location
Ludmila Alexandrova, PhD		Drug discovery support, PK, Metabolite ID		725-9769		ludmilaa at stanford.edu		Bass 024
Karolina Krasinska, MS		Quantitative MS		725-9769		krasin at stanford.edu		Bass 024
Ryan Leib, PhD		Director of Proteomics		725-9769		rdleib at stanford.edu		Bass 024
Fang Liu, PhD		Proteomics		725-9769		fliu7 at stanford.edu		Bass 024
Garvey Mckenzie, BS		Proteomics		725-9769		gmcken1 at stanford.edu		Bass 024
Theresa McLaughlin, MS		Lab Manager, Open access, HRMS, intact protein		725-9769		tmcl at stanford.edu		Bass 024
Norah Brown, MS		Proteomics		725-9769		norahbr at stanford.edu		Bass 024

 

Location and Hours of Operation 

Location	Hours - No drop-ins due to COVID-19. Contact SUMS to make arrangements.
SUMS, 327 Campus Drive Room: 024 Stanford University, Stanford, CA 94305-4401 Phone: (650) 725-9769 Email:  spectrometry@stanford.edu	9 a.m. - 5 p.m., Monday to Friday   24/7 access for trained Open Access users

 

Click to view SUMS location on Stanford Campus Map

 

Links and Resources

• Visit our lab website for more information: https://mass-spec.stanford.edu/

    

Publication Acknowledgement 

In accordance with Dean's office policy: If work done with SUMS produces data in a publication, you must acknowledge us ("Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University Mass Spectrometry") in the publication. Further, if SUMS staff provide significant experimental design, data interpretation, or other intellectual contribution (as evaluated by the PI), then it is expected that these individuals will be coauthors on the publication. 

In addition, please acknowledge the following:

Stanford Cancer Institute: As a Stanford Cancer Institute Shared Resource, our lab receives grant support from the National Cancer Institute, which should be acknowledged in all publications containing data collected at SUMS. The following statement is suggested: “This work was supported in part by NIH P30 CA124435 utilizing the Stanford Cancer Institute Proteomics/Mass Spectrometry Shared Resource.”

The NIH requires that all publications containing data collected on our Shared Instrumentation Grant (SIG) Program funded instruments acknowledge NIH grant support. 

Orbi Elite: "This work utilized the LTQ-Orbitrap mass spectrometer system that was purchased with funding from National Institutes of Health Shared Instrumentation grant S10RR027425."

Xevo TQ-XS: "This work utilized the Xevo TQ-XS mass spectrometer system that was purchased with funding from National Institutes of Health Shared Instrumentation grant S10OD026962."

 

 

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Contacts

Name	Role	Phone	Email	Location
Allis Chien, Ph.D.	Director	650.723.0710	allis at stanford.edu	Bass 026
Ryan Leib, Ph.D.	Director of Proteomics	650.725.9769	rdleib at stanford.edu	Bass 024
Theresa McLaughlin, M.S	Lab Manager, Open Access	650.725.9769	tmcl at stanford.edu	Bass 024
William Lee	Finance	650.725.9769	wlee2 at stanford.edu	Bass 024