Stanford University Mass Spectrometry

 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.


Save the date!

Thursday October 4, 2018

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 15 instruments in operation: three GC-MS and eleven LC-MS systems -- four single quads, one ion trap, four triple quads, one hybrid quadrupole-time of flight, one benchtop Orbitrap and three hybrid LTQ-Orbitraps -- 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 LCquan, QuanLynx, OpenLynx, MetaboLynx, ChemStation, Mass Hunter, Spectral Works.

Routine mass spec and proteomic services include molecular weight determination, MSn, LC-MS, 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 characterization - intact mass, peptide mapping
    • Protein interactions - SNAP, crosslinking
  • Small Molecules
    • Molecular weight confirmation
    • High resolution molecular formula confirmation (HRMS)
    • Structural elucidation (MSn)
    • Targeted quantitation
  • 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 of interest
  • Metabolomics
    • Targeted, Quantitative
    • Semi-Quantitative
  • Open access (Stanford Users Only)
    • LC-MS
    • GC-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.


Allis Chien, PhD | SUMS Director

Office (Mudd 167A):  (650) 723-0710

Lab    (Mudd 175):  (650) 725-9769

Email:  allis at












William Lee


Financial Contact




wlee2 at


Mudd 167B

Chris Adams, PhD


Director of Proteomics




adamscm at


Mudd 167A

Ludmila Alexandrova, PhD


Drug discovery support, PK, Metabolite ID




ludmilaa at  


Mudd 167B

Karolina Krasinska, MS


Quantitative MS




krasin at


Mudd 167B

Ryan Leib, PhD






rdleib at


Mudd 167B

Theresa McLaughlin, MS


Lab Manager, HRMS, Open access lab, Custom projects




tmcl at


Mudd 167A

Kratika Singhal, MS






ksingh29 at


Mudd 167B



Location and Hours of Operation 



SUMS, 333 Campus Drive, MUDD 175, MC 5080

Stanford University, Stanford, CA 94305-4401

Phone: (650) 725-9769

Fax:  (650) 725-0259


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:

NIH requirement for Orbi data: Each publication, press release or other document that uses data from the LTQ-Orbitrap Velos instrument must include an acknowledgement of NIH grant support and disclaimer such as the following:  "The project described was supported by Award Number S10RR027425 from the National Center for Research Resources. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Center for Research Resources or the National Institutes of Health."


Stanford Cancer Institute acknowledgement:  As a Stanford Cancer Institute Shared Resource, our lab receives grant support from the National Cancer Institute, which should be acknowledged in all publications. 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.


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Name Role Phone Email Location
Allis Chien, Ph.D.
allis at
Mudd 167A
Theresa McLaughlin, MS
Lab Manager
tmcl at
Mudd 167B
William Lee
wlee2 at
Mudd 167B


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