Descriptions of the Proteomics Resource Center

The Proteomics Resource Center (RRID:SCR_017797) is directed by Henrik Molina, Ph.D. who oversees a staff of six scientists.  Dr. Molina’s experience is based on more than two decades working in most aspects of mass spectrometry based proteomics, 100+ publications, five years in the biotech industry, six years at The Johns Hopkins University and three years as the Director of the Proteomics Unit at the Center for Genomic Regulation in Barcelona, Spain, prior to his arrival at the University in 2011. The Center’s team is composed of highly skilled and devoted scientist with experience in proteomics, analytical chemistry and informatics.

The Proteomics Resource Center at The Rockefeller University masters most aspects of mass spectrometry based proteomics which includes, denovo sequencing ¹,  targeted studies ², quantitative proteomics profiling based on label free quantitation ³ as well as metabolic labelled samples (SILAC) ⁴, chemical labeling ⁵, tandem-mass tag technology ^6,7, absolute quantitation ⁸ and global post translational analysis ^{9, 10}.  The Center also offers LC-MS based analysis of small molecules ¹¹, polar metabolites ¹² and lipids ¹³. Very importantly, the Center is a source for help with planning of mass spectrometry based experiments and the Center have the capability to offer in-depth collaborative analysis. Also, the PRC is operated in a boutique style; encouraging the scientists of the Center to work closely with users to create a tailored approach to fit the many unique questions that can be answered by analytical mass spectrometry.

The PRC are equipped with Orbitrap type mass spectrometers (high resolution/high mass accuracy), operates a triple quadrupole and can separate analytes using both nano and high flow liquid chromatography. The Center is equipped with multiple high performance servers for data analysis.

The Center occupies over 3000 sq. ft. of lab space located on the Rockefeller campus on the Upper East Side of Manhattan, in proximity to Weill-Cornell Medical College and Memorial-Sloan Kettering Cancer Center. On a yearly basis, the Center works with close to 200 users and logs more than 6,000 hours of mass spec analysis.

1. Hover, B.M. et al. Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens. Nature microbiology (2018).
2. Maze, I. et al. Critical Role of Histone Turnover in Neuronal Transcription and Plasticity. Neuron 87, 77-94 (2015).
3. Hoshino, A. et al. Tumour exosome integrins determine organotropic metastasis. Nature 527, 329-335 (2015).
4. Goodarzi, H. et al. Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. cell 165, 1416-1427 (2016).
5. Kung, A. et al. Development of Specific, Irreversible Inhibitors for a Receptor Tyrosine Kinase EphB3. J Am Chem Soc (2016).
6. Bunkenborg, J., Espadas, G. & Molina, H. Cutting edge proteomics: benchmarking of six commercial trypsins. J Proteome Res 12, 3631-3641 (2013).
7. Hong, S. et al. Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion. Nature medicine (2016).
8. Duvall, L.B., Basrur, N.S., Molina, H., McMeniman, C.J. & Vosshall, L.B. A Peptide Signaling System that Rapidly Enforces Paternity in the Aedes aegypti Mosquito. Curr Biol (2017).
9. Govek, E.E. et al. Cdc42 Regulates Neuronal Polarity during Cerebellar Axon Formation and Glial-Guided Migration. iScience 1, 35-48 (2018).
10. Garzia, A. et al. The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. Nature communications 8, 16056 (2017).
11. Lood, R., Molina, H. & Fischetti, V.A. Determining bacteriophage endopeptidase activity using either fluorophore-quencher labeled peptides combined with liquid chromatography-mass spectrometry (LC-MS) or Forster resonance energy transfer (FRET) assays. PLoS ONE 12, e0173919 (2017).
12. Garcia-Bermudez, J. et al. Aspartate is a limiting metabolite for cancer cell proliferation under hypoxia and in tumours. Nature cell biology 20, 775-781 (2018).
13. Zhu, X.G. et al. CHP1 Regulates Compartmentalized Glycerolipid Synthesis by Activating GPAT4. Mol Cell (2019).

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