Proteomics and Metabolomics Core Facility


  • Note: due to the high number of service requests, the current turnaround time is ~3 weeks for most assays, 4-6 weeks for TMT projects.
  • 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 *
      • 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. )
    • 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 (Note: minimum 6 samples. See the list HERE.)
      • Type 1: positive ion mode (CE, Cer, DG, LPC, LPE, PC, PE, PI, PS, SM, TG)
      • Type 2: positive and negative ion mode (CL, PA, PG, CE, Cer, DG, LPC, LPE, PC, PE, PI, PS, SM, TG)
    • Free fatty acid profiling  (See the list HERE.)
    • Acylcarnitine profiling  (See the list HERE.)
    • Short chain Acyl-CoAs  (See the list HERE.)


    • Unless otherwise noted, quantitation in all assays is relative quantitation, not absolute.
    • For quantitative analysis, please submit all samples together to minimize variation. It is difficult to compare data acquired at different times.
    • Turnaround time is normally 5-10 business days, except for TMT global protein/PTM profiling (~4 weeks).
    • Assays marked with *: Standard statistical analysis (such as heatmap, PCA, t-test, one-way anova) may be included in the report for free when appropriate. Additional customized data analysis requests will incur charges. Free software tools are available to avoid such charges (e.g. Metaboanalyst for metabolomics, Perseus for proteomics).

What's in the Report

Sample Preparation Protocols


  • Click HERE to see pricing for Fiscal Year 2024
  • Note: service fees are adjusted annually to reflect changes in running cost

Service Request Workflow

  1. Create a service request on iLab
  2. Get a quote from the core
  3. Approve the cost in iLab
  4. Financial approval in iLab by PI or a designated financial admin / lab manager
  5. Drop off samples to the core (by email appointment only; after finacial approval only)
  6. Sample analysis by the core
  7. Receive analysis results
  8. Receive invoices
  9. Payment (external users pay with PO; internal users with WCM funds)

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

Agilent QQQ MS


timsTOF Pro 2

Bruker timsTOF Pro 2


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
guz2004 [at]
Phone (646) 962-6222

Dr. Mengmeng Zhu - mez2005 [at]
Dr. Xiaoyuan Yang - xiy4003 [at]
Dr. Zhucui Li - zhl4007 [at]
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 between 10:30am - 4pm. Call 646-962-9739 to get into the glass door when arriving at 15th floor. For shipping, please use overnight shipping on dry ice and notify the core of the trackinng number.)

Note:  for all sample drop-off, please schedule a time in advance with core staff by email.

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