Development in liquid chromatography, mass spectrometry, and related technologies
Despite the growing use of mass spectrometry in biomedical research, the wide dynamic range of protein expression and varying stoichiometry of post-translational modifications represent a significant hurdle to achieving 'unbiased' proteome characterization. This limitation remains even in the face of intense, ongoing commercial R&D efforts to improve the performance of modern mass spectrometry hardware and develop more sophisticated software for embedded system control. The absence of a chemical amplification strategy for proteins (e.g., PCR) places a premium on the integration of efficient peptide fractionation or other separation techniques with mass spectrometry for bottom-up proteomic applications. We have developed, systematically optimized, and applied high-performance liquid chromatography assemblies for fully automated single- and multiple-dimension peptide separation coupled directly to mass spectrometry; these platforms provide improved detection, dynamic range, and quantification. Cognizant of the growing importance of translational studies, we continue to refine and re-engineer these systems to improve performance and reduce sample consumption, with a primary objective of using quantitative mass spectrometry for the analysis of high-fidelity model systems and primary human tissues. Related research efforts include synthesis of novel multiplexed stable isotope reagents, as well as methods to improve the enrichment and analysis of protein post-translational modifications. See papers below and our resources page for more information.
Publications related to technology development
17. Browne CM, Jiang B, Ficarro SB, Doctor ZM, Johnson JL, Card JD, Sivakumaren SC, Alexander WM, Yaron TM, Murphy CJ, Kwiatkowski NP, Zhang T, Cantley
LC, Gray NS, Marto JA. A chemoproteomic strategy for direct and proteome-wide covalent inhibitor target-site identification. J Am Chem Soc
16. Kang UB, Alexander WM, Marto JA. Interrogating the hidden phosphoproteome. Proteomics 2017;17:1600437§.
15. Ficarro SB, Browne CM, Card JD, Alexander WM, Zhang T, Park E, Paganon SD, Seo HS, Lamberto I, Eck MJ, Buhrlage SJ, Gray NS, Marto JA. Leveraging
novel fragmentation pathways for improved identification and selective detection of targets modified by covalent probes. Anal Chem 2016;88:12248-54.
14. Suh H, Ficarro SB, Kang UB, Chun Y, Marto JA, Buratowski S. Direct analysis of phosphorylation sites on rbp1 c-terminal domain of rna polymerase II.
Mol Cell 2016;61:297-304.
13. Ficarro SB, Biagi JM, Wang J, Scotcher J, Koleva RI, Card JD, Adelmant G, He H, Askenazi M, Marshall AG, Young NL, Gray NS, Marto JA. Protected amine
labels: a versatile molecular scaffold for multiplexed nominal mass and sub-da isotopologue quantitative proteomic reagents. J Am Soc Mass Spectrom
12. Zhou F, Lu Y, Ficarro SB, Adelmant G, Jiang W, Luckey CJ, Marto JA. DEEP SEQ mass spectrometry: a platform for genome-scale proteome quantification.
Nat Comm 2013;4:2171.
11. Zhou F, Lu Y, Ficarro SB, Webber JT, Marto JA. A nanoflow low pressure high peak capacity single dimension lc-ms/ms platform for in-depth analysis of
mammalian proteomes. Anal Chem 2012;84:5133-9.
10. Savitski MM, Sweetman G, Askenazi M, Marto JA, Lang M, Zinn N, Bantscheff M. Delayed fragmentation and optimized isolation width settings improve
protein identification and accuracy of isobaric mass tag quantification on orbitrap-type mass spectrometers. Anal Chem 2011;83:8959-67.
9. Ficarro SB, Zhang Y, Alfonso MC, Adelmant GO, Garg B, Webber JT, Luckey CJ, Marto JA. Online nanoflow mult-dimensional fractionation strategies for
high efficiency phosphopeptide analysis. Mol Cell Proteomics 2011;10:M111.011064, 1-19.
8. Zhou F, Sikorski TW, Ficarro SB, Webber JT, Marto JA. An online nanoflow rp-sax-rp lc-ms/ms platform for efficient and in-depth proteome sequence
analysis of complex organisms. Anal Chem 2011;83:6996-7005.
7. Zhou F, Cardoza JD, Ficarro SB, Adelmant GO, Lazaro JB, Marto JA. Online nanoflow rp-rp-ms reveals dynamics of mult-component ku complex in
response to dna damage. J Proteome Res 2010;9:6242-55.
6. Ficarro SB, Adelmant G, Tomar MN, Zhang Y, Cheng VJ, Marto JA. Magnetic bead processor for rapid evaluation and optimization of parameters for
phosphopeptide enrichment. Anal Chem 2009;81:4566-75.
5. Zhang Y, Ficarro SB, Li S, Marto JA. Optimized Orbitrap HCD for quantitative analysis of phosphopeptides. J Am Soc Mass Spectrom 2009;20:1425-34.
4. Ficarro SB, Zhang Y, Lu Y, Moghimi AR, Askenazi M, Hyatt E, Smith ED, Boyer L, Schlaeger TM, Luckey CJ, Marto JA. Improved electrospray ionization
efficiency compensates for diminished chromatographic resolution and enables proteomics analysis of tyrosine signaling in embryonic stem cells. Anal
3. Phanstiel D, Zhang Y, Marto JA, Coon JJ. Peptide and protein quantification using iTRAQ with electron transfer dissociation. J Am Soc Mass Spectrom
2. Ficarro SB, Parikh JR, Blank NC, Marto JA. Niobium(V) oxide (Nb2O5): application to phosphoproteomics. Anal Chem 2008;80:4606-13.
1. Ndassa YM, Orsi C, Marto JA*, Chen S, Ross MM. Improved immobilized metal affinity chromatography for large-scale phosphoproteomics applications.
J Proteome Res 2006;5:2789-99.