NYU Langone’s Proteomics Laboratory provides investigators with the latest technologies. These technologies include but are not limited to the following:

• comprehensive proteome characterization
• characterization of post-translational modifications
• characterization of affinity purified complexes to identify interaction partners
• label-free relative quantitation of proteins isolated from affinity purifications, entire organisms, whole-cell extracts, secretomes, or tissue sections
• label-free relative quantitation of post-translational modifications, usually after enrichment steps (such as phosphorylation [serine, threonine or tyrosine], ubiquitination)
• Metabolic (stable isotope labeling using amino acids in cell culture [SILAC]) or chemical (tandem mass tag [TMT]) labeling for relative quantitation of proteins and post-translational modifications isolated from whole-cell extracts, tissues, or entire organisms 
• absolute quantitation using stable isotope labeled synthetic peptide standards
• targeted quantitation with or without internal stable isotope peptide standards
• de novo sequencing
• characterization of higher-order structure
• protein or peptide fractionation prior to mass spectrometric analysis 
• custom projects

Mass Spectrometers

Our laboratory is equipped with three high-resolution mass spectrometers offering four types of peptide fragmentation:

• ion trap collisionally activated dissociation (CAD)
• beam-type collisionally activated dissociation (HCD)
• electron-transfer dissociation (ETD)
• electron-transfer/higher-energy collisional dissociation (EThcD)

Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer 

The Thermo Scientific Q Exactive^™ Hybrid Quadrupole-Orbitrap^™ Mass Spectrometer is coupled to a nanoflow EASY-nLC^™ HPLC. It enables quadrupole precursor isolation with high-resolution, accurate mass detection. The instrument performs HCD peptide fragmentation. It supports label and label-free quantitation and multiplexed relative quantitation using isobaric tags. 

Thermo Scientific Orbitrap Elite Hybrid Ion Trap-Orbitrap Mass Spectrometer 

The Thermo Scientific Orbitrap Elite^™ Hybrid Ion Trap-Orbitrap Mass Spectrometer with electron transfer dissociation is coupled to a nanoflow EASY-nLC^™ HPLC. This hybrid instrument has two detectors, the ion trap and Orbitrap. It offers three dissociation techniques: CAD, HCD, and ETD. It can perform high- or low-resolution acquisition in MS1 and MS/MS scans. HCD is enabled only in the high-resolution mode.  

Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer 

The Thermo Scientific Orbitrap Fusion^™ Lumos^™ Tribrid^™ Mass Spectrometer with electron transfer dissociation is coupled to a nanoflow EASY-nLC^™ HPLC. This hybrid instrument has two detectors, the ion trap and the Orbitrap. It offers four dissociation techniques: CAD, HCD, ETD, and EThcD. It can be used for high- or low-resolution acquisition and supports intact protein analysis. 

In addition, the instrument supports label and label-free quantitation and multiplexed relative quantitation using isobaric tags.