Herbert Irving Comprehensive Cancer Center
Flash Section


Emily Chen, Ph.D., Director

Antonius A. Koller, Ph.D., Manager

ICRC, 1130 Saint Nicholas Ave, 10th Floor

Mass Spectrometry Proteomics

The Proteomics Shared Resource supports both discovery-based and targeted proteomic analysis. The facility provides cancer researchers access to the state-of-the-art mass spectrometers and software for qualitative (e.g. protein identification), quantitative (e.g. relative quantification), and post-translational modification (PTM) analyses. The services include i) mass determination of purified proteins/peptides, ii) identification of purified protein complexes, iii) site-targeted PTM mapping on purified proteins, targeted MRM quantification, iv) global proteome analysis, subproteome isolation and identification, and v) large-scale PTM characterization. The facility director and dedicated technical personnel have extensive expertise in mass spectrometry-based techniques and will provide consultation on experimental design, data analysis, and troubleshooting. We encourage researchers to contact us prior to submission of samples to discuss sample preparation, experimental design, and potential outcomes of research projects.

To all Proteomics SR users: Beginning October 20, the Proteomics SR will use the iLab Core Management System for service requests and billing. More information for users, PIs, and Financial Managers can be found here. To schedule equipment and make service requests, go to the iLab web site at https://cumc.corefacilities.org and log in with your UNI and password. To schedule equipment and make service requests, go to the iLab web site at https://cumc.corefacilities.org and log in with your UNI and password.

Specific services provided

  • Sample preparation for mass spectrometry-based proteomic analysis (total lysate, subcellular fractionation, affinity enrichment for PTM peptides, etc.)
  • Protein quantification for proteomic analysis
  • Chemical labeling, profiling, and quantification (e.g. iTRAQ, TMT, etc.)
  • Profiling and quantification of metabolically labeled cells and tissues (e.g. SILAC, SILAM, etc.)
  • Gel band cutting and protein identification
  • Protein expression profiling of tissues (fresh frozen and FFPE tissues)
  • Large-scale PTM characterization (e.g. phosphorylation, ubiquitination, acetylation, etc.)
  • Targeted protein/peptide characterization/quantification (customized MRM)
  • High-throughput protein identification in complex biological samples
  • Method development for innovative projects
  • Statistical analysis and data mining for large-scale proteomics projects


  • Fusion Tribrid Mass Spectrometer + Easy-nLC 1000 (Thermo) (http://www.thermoscientific.com/ecomm/servlet/productsdetail_11152_L10816_87170_16235543_-1)
  • UltrafleXtreme MALDI TOF/TOF (Bruker)
  • SpectraMax Gemini plate reader (Molecular Devices)
  • Air Clean 600 workstation for sample preparation
  • Omni Bead Ruptor Homogenizer for sample preparation


  • Proteome Discoverer & Protein Pilot (Database search)
  • Scaffold (Data processing & visualization)
  • Ingenuity Pathway Analysis & MetaCore (Data mining)
  • QLUCORE (Statistical analysis & data visualization)