Typical Projects

The PRC offers a wide variety of LC-MS and LC-MS/MS analyses. Some, but not all, are listed below and include proteomics and metabolomic mass spectrometry based experiments. References for some analyzes are included.

• 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 either PRM ⁴ or MRM ⁵.
• SDS-PAGE gel band analysis.
• De-novo sequencing of peptides ⁶.
• N- and C-terminal mapping of proteins ⁷.
• PTM analysis ^8,9,10.
• Analysis of polar metabolites* ¹¹.
• Nucleoside analysis ¹².
• Analysis of small drugs ⁵.
• Data Dependent lipid profiling* ¹³.
• Aldehyde analysis based on derivation ¹⁴.
• Neurotransmitter analysis.
• Analysis of HLA-type peptides.

*) currently only available for internal groups.

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. Bellat, V. et al. Functional Peptide Nanofibers with Unique Tumor Targeting and Enzyme-Induced Local Retention Properties. Advanced functional materials 28 (2018).
6. 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).
7. Li, H. et al. Zika Virus Protease Cleavage of Host Protein Septin-2 Mediates Mitotic Defects in Neural Progenitors. Neuron (2019).
8. Tang, Z. et al. SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53. cell 154, 297-310 (2013).
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. 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).
12. Westcott, N.P., Fernandez, J.P., Molina, H. & Hang, H.C. Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress. Nat Chem Biol (2017).
13. Zhu, X.G. et al. CHP1 Regulates Compartmentalized Glycerolipid Synthesis by Activating GPAT4. Mol Cell (2019).
14. Matsumura, Y. et al. Gene Therapy Correction of Aldehyde Dehydrogenase 2 Deficiency. Molecular therapy. Methods & clinical development 15, 72-82 (2019).