WCM Proteomics and Metabolomics Core Facility


  • Note: due to the pandemic, for sample drop-off, please schedule a time in advance with core staff to ensure that someone will be in the lab.
  • June 2022 Upgraded proteomic profiling assay using Data Independent Acquisiton (DIA) enables deep coverage and accurate quantitation without the need of isotope labeling.


Established in 2016, the Weill Cornell Medicine (WCM) Meyer Cancer Center Proteomics and Metabolomics Core Facility offers mass spectrometry-based analysis of proteins, peptides, metabolites and other biochemical molecules, to Weill Cornell Medicine users as well as external users from academic institutions and commercial enterprises.

  • Proteomics
    • Proteomic profiling by label-free quantitation
      • Label-free quantitation enables straightforward experimental design. 
      • With improved data independend acquisition (DIA) methods, typical number of protein IDs ranges 5,000-7,000 for human/mouse total cell lysate.
      • Popular applications: protein expression profiling; protein interactions (IP); proximity-based labeling for interactome mapping (APEX) etc. 
    • Proteomic and phosphoproteome profiling by TMT quantitation (See a Sample report. )
      • Stable isotope labeling enables high accuracy in quantitation. Ideal for deep coverage phosphoproteome analysis.
      • Allows comparing up to 18 samples in a single experiment.
      • Typical number of protein IDs 6,000-8,000, phosphosites 10,000 - 20,000 for human/mouse total cell lysate.
      • Popular applications: global phosphoproteomics; Thermo Proteome Profiling (TPP)/Cellular Thermal Shift Assay (CETSA), etc. 
    • Post-Translational Modification (PTM) analysis
      • Popular applications: PTM characterization of purified protein; histone modifications profiling(See details HERE); crosslinking proteomics, etc.
      • Types of PTM include: Phosphorylation, ubiquitination, acetylation, N/C-term processing, etc.
    • Identification of gel purified proteins
                 Popular applications: confirmation of protein expression, etc.
  • Metabolomics
    • Targeted profiling of polar metabolites (Targeted detection of metabolites in a predefined panel, which includes many central metabolites such as glycolysis/TCA intermediates and amino acids. See the list HERE. See a Sample report. )
    • Stable isotope tracing / flux for polar metabolites (e.g. C13 glucose labeling. See a Sample report. )
      • Type 1: Tracing of selected metabolites (Please select metabolites from the LIST to avoid ambiguity.)
      • Type 2: Full panel tracing (Exhaustive tracing of all detected metabolites. No need to know beforehand if a particular metabolite is labeled or not. Note: minimum 6 samples) 
    • Untargeted metabolite profiling (See details HERE.)
    • Lipid profiling (See the list HERE.)
    • Free fatty acid profiling  (See the list HERE.)
    • Bile acids  (See the list HERE.)
    • Acylcarnitine profiling  (See the list HERE.)
    • Short chain Acyl-CoAs  (See the list HERE.)
    • Folate metabolites  (See the list HERE.)
    • Thyroid hormones triiodothyronine/thyroxine (T3/T4) absolute quantitation (100 ul serum is needed)
    • Targeted analysis of 7 polyamines (See the list HERE.)
    • Accurate MW measurement (HRMS) for drugs/chemicals (mass accuracy: a few ppm)
    • New method development


    • Unless otherwise noted, quantitation in all assays is relative quantitation, not absolute.
    • Turnaround time is normally 5-10 business days, except for global protein/PTM profiling (~4 weeks).

Sample Preparation Protocols


  • Click HERE to see pricing
  • Note: service rates are adjusted annually to reflect changes in running cost

Service Request

Note: All service requests are done via the online iLab system. An iLab account is needed for sample submissions.


             Orbitrap Fusion Lumos

    Orbitrap Q Exactive / Vanquish UPLC

  • Easy-nLC 1200 UPLC 
  • Agilent 1260 

timsTOF Pro 2

Bruker timsTOF Pro 2

  • High sensitivity mass spectrometer for label-free proteomics


Links and Resources

  • To acknowledge the core in a publication
    • Mass spectrometric analysis was (analyses were) performed at the Weill Cornell Medicine Proteomics and Metabolomics Core Facility.
  • Report format

Contact Us

Guoan Zhang PhD
Phone (646) 962-6222

Dr. Mengmeng Zhu - mez2005@med.cornell.edu
Dr. Xiaoyuan Yang - xiy4003@med.cornell.edu
Phone (646) 962-9739

Sample Drop-off / Shipping Address

413 East 69th Street, BRB 1552 (Zhang lab)
New York, NY 10021
Lab phone: 646-962-9739

(For sample drop off, please drop off to Lab 1552 of Belfer building. Call 646-962-9739 to get into the glass door when arriving at 15th floor.)

Note: due to the pandemic, for all sample drop-off, please schedule a time in advance with core staff to ensure that some one will be in the lab.

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