Welcome to the BIDMC Mass Spectrometry Facility

'Specializing in a directed proteomics & metabolomics approach towards cellular signaling'

ABOUT USThe mass spectrometry, proteomics, metabolomics and lipidomics facility at Beth Israel Deaconess Medical Center was established in 2004 led by Dr. John Asara and continues to grow rapidly. We provide excellent proteomics and metabolomics services with low prices and fast turnaround times. We have cutting edge instruments operated at optimal sensitivity and work and publish with world class researchers. We also maintain an active internal cancer proteomics and metabolomics research program with collaborative efforts. Our expertise is in identifying and quantifying protein modifications and dynamic protein-protein interactions in addition to polar metabolomics profiling, flux analysis and lipidomics profiling. We accept collaborations from anywhere in the world and look forward to helping you and progressing your research to the next level.


  • We have just upgraded our proteomics/phosphoproteomics platform with an ultra fast and ultra sensitive Thermo QExactive HF via the BIDMC Capital Equipment Award
  • Our Lipidomics profiling platform is now operating on the Thermo QExactive Plus with LipidSearch software
  • We just installed a QExactive Plus Orbitrap high resolution mass spectrometer for a future lipidomics and untargeted metabolomics platform (This is considered one of Thermo's fastest and most sensitive instruments)
  • We recently installed a NIH funded Thermo Velos Elite Orbitrap Mass Spectrometer (Ultra high resolution, deep proteome coverage, extremely sensitive)
  • We have lowered our prices for external academic users, corporate users for large orders with more than 10 samples


Proteomics, Metabolomics & Lipidomics

  • Protein Complex Identification
    (protein complexes, protein-protein interactions, single protein ID)
  • Identification of Post-Translational Modifications
    (phosphorylation, acetylation, ubiquitination, etc.)
  • Relative Protein Quantification
    (MS1 based label-free quantification, SILAC, Avg. TIC, TMT, etc.)
    • Protein complex stoichiometry
    • Quantification of phosphorylation sites
    • PPI networks 
  • Quantitative Metabolomics Profiling  
    (endogenous polar metabolites from any cell or tissue source) 
    • Steady-state profiling
    • C13/N15 metabolic flux analysis
  • Lipidomics Profiling
  • (High resolution, identification of most lipid classes and molecules through fragmentation, high throughput from any biological source)                              


  • Thermo Scientific QExactive HF (ultra fast and ultra sensitive for proteomics, etc.)
  • Thermo Scientific QExactive Plus Orbitrap (high resolution, extremely fast scan speeds, HCD fragmentation, quantitative)
  • Thermo Scientific Elite Orbitrap(ultra-high resolution and fast scan speed, extremely sensitive, CID and HCD fragmentation)
  • Thermo Scientific LTQ Orbitrap XL-ETD
    (high resolution and mass accuracy, HCD collision cell, ETD fragmentation for labile modifications)
  • AB/SCIEX 5500 QTRAP triple quadrupole
    (Metabolomics profiling, targeted quantification)
  • Proxeon EASY-nLC II (3)
    (nanoliter flow rates, very reproducible and robust)
  • Shimadzu Prominence UFLC
  • Michrom Bioresources Paradigm 2D-HPLC
  • Agilent 1200 HPLC
Thermo Scientific QExactive Plus

 Thermo Scientific Elite Orbitrap

Thermo Scientific LTQ Orbitrap XL-ETD


Thermo (Proxeon) EASY-nLC II (3)






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