The rockefeller university

Around 2008 the focus of the Center shifted from using Edman sequencing to mass spectrometry for the analysis of proteins. Mass spectrometry was later combined with liquid chromatography using electrospray.  Currently, the Center operates all Orbitrap  based high resolution high mass accuracy (HRMS) LC-MS/MS  mass spectrometers coupled to reversed phase nano-flow flow liquid chromatography.

The team has extensive experience with a wealth of LCMS based technologies for the identification and quantitation of peptides and proteins.  Typical projects analyzed by the Center includes:

• Mass spectrometry based affinity purification analysis (aka co-IPs, pulldowns) ¹.
• Profiling, quantitative as well as qualitative, of complex samples ^{2, 3}.
• Targeted analysis using PRM ⁴ .
• SDS-PAGE gel band analysis.
• De-novo sequencing of peptides ⁵.
• N- and C-terminal mapping of proteins ⁶.
• PTM analysis ^7,8,9.
• Neurotransmitter analysis.
• Analysis of HLA-type peptides ¹⁰.

References

1. Li, M.M. et al. TRIM25 Enhances the Antiviral Action of Zinc-Finger Antiviral Protein (ZAP). PLoS pathogens 13, e1006145 (2017).
2. Goodarzi, H. et al. Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. cell 165, 1416-1427 (2016).
3. Hoshino, A. et al. Tumour exosome integrins determine organotropic metastasis. Nature 527, 329-335 (2015).
4. Wang, A.T. et al. A Dominant Mutation in Human RAD51 Reveals Its Function in DNA Interstrand Crosslink Repair Independent of Homologous Recombination. Mol Cell 59, 478-490 (2015).
5. 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).
6. Li, H. et al. Zika Virus Protease Cleavage of Host Protein Septin-2 Mediates Mitotic Defects in Neural Progenitors. Neuron (2019).
7. Tang, Z. et al. SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53. cell 154, 297-310 (2013).
8. Govek, E.E. et al. Cdc42 Regulates Neuronal Polarity during Cerebellar Axon Formation and Glial-Guided Migration. iScience 1, 35-48 (2018).
9. 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).
10. Klatt, M.G.. et al. Solving an MHC allele-specific bias in the reported immunopeptidome. JCI Insight. 19, (2020).