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
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Role
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Slack Username
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Email (@stanford.edu)
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Location
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Ludmila Alexandrova, PhD
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Drug discovery support, PK, Metabolite ID
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ludmila_alexandrova
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ludmilaa@
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Bass 024
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Norah Brown, MS
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Proteomics
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norah_brown
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norahbr@
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Bass 024
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Megan Danielewicz, PhD
Karolina Krasinska, MS
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Metaolomics, Quantitative MS
Quantitative MS
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m3g4n
karolina_krasinska
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m3g4n@
krasin@
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Bass 024
Bass 024
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Fang Liu, PhD
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Proteomics
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fliu7
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fliu7@
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Bass 024
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Garvey Mckenzie, BS |
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Proteomics
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gmcken1
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gmcken1@
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Bass 024
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Theresa McLaughlin, MS
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Lab Manager, Open access, HRMS, intact protein
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theresa_mclaughlin
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tmcl@
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Bass 024
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Casey Schmidt, PhD
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Education, Proteomics |
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casey_schmidt
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capowers@
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Bass 024
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Location and Hours of Operation
Location
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Hours - Contact SUMS to make arrangements.
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SUMS, 327 Campus Drive
Room: 024
Stanford University, Stanford, CA 94305-4401
Phone: (650) 725-9769
Email: spectrometry@stanford.edu
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9 a.m. - 5 p.m., Monday to Friday
24/7 access for trained Open Access users
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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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