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Stanford University Mass Spectrometry


Save the date: Thursday October 17, 2024


SUMS Weekly Office Hours

Have a question about a potential mass spec project? Not sure exactly who to talk with at SUMS?
Drop in to our open virtual Zoom office on Thursday afternoons between 4:00 and 4:30 pm Pacific Time and get answers! Or email us at spectrometry@stanford.edu


 

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.

We have numerous instruments in operation: one GC-MS, a MALDI-TOF, and many LC-MS systems, including a single quad, four triple quads, four quadrupole-Orbitraps, and two Orbitrap tribrids. Software resources include instrument-specific packages Xcalibur, MassLynx, Mass Hunter; proteomics software Byonic, Mascot, Proteome Discoverer; and other tools including LCquan, QuanLynx, OpenLynx, MetaboLynx, 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

 

Slack Username

 

Email (@stanford.edu)

 

Location

Ludmila Alexandrova, PhD

 

Drug discovery support, PK, Metabolite ID

 

ludmila_alexandrova

 

ludmilaa@

 

Bass 024

Norah Brown, MS

 

Proteomics

 

norah_brown

 

norahbr@

 

Bass 024

Megan Danielewicz, PhD

Karolina Krasinska, MS

 

Metaolomics, Quantitative MS

Quantitative MS

 

m3g4n

karolina_krasinska

 

m3g4n@

krasin@

 

Bass 024

Bass 024

Fang Liu, PhD

 

Proteomics

 

fliu7

 

fliu7@

 

Bass 024

Garvey Mckenzie, BS

 

Proteomics

 

gmcken1

 

gmcken1@

 

Bass 024

Theresa McLaughlin, MS

 

Lab Manager, Open access, HRMS, intact protein

 

theresa_mclaughlin

 

tmcl@

 

Bass 024

Casey Schmidt, PhD

 

Education, Proteomics

 

casey_schmidt

 

capowers@

 

Bass 024

 

 

Location and Hours of Operation 

Location

Hours - 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

    

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 Thermo LTQ-Orbitrap mass spectrometer system (RRID:SCR_018694) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant S10RR027425."

Xevo TQ-XS: "This work utilized the Waters Xevo TQ-XS mass spectrometer system (RRID:SCR_018510) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant S10OD026962."

Orbi Eclipse: "This work utilized the Thermo Orbitrap Eclipse nanoLC/MS system (RRID:SCR_022212) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant 1S10OD030473."

6495 Triple Quad: "This work utilized the Agilent 6495 Triple Quadrupole LC/MS system (RRID:SCR_023937) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant 1S10OD034374."

 

RRIDs for non-NIH funded instruments:

  • Agilent 7890/5975 GC/MS system (RRID:SCR_018695)
  • Bruker Microflex MALDI TOF mass spectrometer (RRID:SCR_018696)
  • Bruker micrOTOF-Q II LC/MS system (RRID:SCR_018697)
  • Bruker Scion TQ GC/MS mass spectrometer (RRID:SCR_018698)
  • Shimadzu 8030 LC/MS mass spectrometer (RRID:SCR_018699)
  • Thermo Exactive Orbitrap LC/MS system (RRID:SCR_018700)
  • Thermo Exploris 240 LC/MS system (RRID:SCR_022216)
  • Thermo Exploris 480 nanoLC/MS system (RRID:SCR_022215)
  • Thermo LTQ-Orbitrap Elite nano LC/MS system (RRID:SCR_018694)
  • Thermo LTQ XL LC/MS system (RRID:SCR_018701)
  • Thermo Orbitrap Fusion nanoLC/MS system (RRID:SCR_018702)
  • Thermo QE-HFX mass spectrometer (RRID:SCR_018703)
  • Thermo Vantage LC/MS system (RRID:SCR_018704)
  • Waters Quattro Premier LC/MS system (RRID:SCR_018705)
  • Waters SQD2 LC/MS system (RRID:SCR_022217)
  • Waters Select Series Cyclic IMS (RRID:SCR_023939)
  • Waters Select Series MRT (RRID:SCR_023938)

 

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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 Research
 
650.725.9769
 
rdleib at stanford.edu
 
Bass 026
 
Fang Liu, Ph.D.
Director of Proteomics
 
650.725.9769
 
fliu7 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
 
650.725.9759
 
wlee2 at stanford.edu
 
Bass 024