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Professor, Chemistry Department

Professor Reilly received his A.B., Chemistry, from Princeton University in 1972. He completed his PhD in Physical Chemistry at the University of California, Berkeley in 1977. He served as a postdoctoral fellow in 1978 at Max-Planck under the tutelage of Gesellschaft Zur Forderung Der Wissenschaften. Professor Reilly has been a member of the Indiana University, Department of Chemistry, faculty since 1979.

In addition Professor Reilly was selected to be the recipient of the Alfred P. Sloan Fellowship in 1982; Camille and Henry Dreyfus Teacher-Scholar Award, 1983; in 1998 and 1999, he received an Indiana University Departmental Teaching Excellence Award; and more recently, he received an Indiana University Trustee Teaching Award in 2005.

Research

Our research interests focus on the following areas:

1. Efficient biomolecular ion production. Biological samples tend to be complex, and it is a challenge to detect molecules of particular interest when they are surrounded by an abundance of background. We investigate selective capture of molecules on surfaces and develop molecular derivatizations to enhance ion yields

2. Proteomics. Chromatographic and electrophoretic fractionation of cellular lysates, robotically controlled sample preparation and MALDI and electrospray ionization mass spectrometry are used to analyze the protein constituents of cells. Proteins are identified by their molecular weights and isoelectric points, through peptide mass maps and by sequencing proteolytically generated representative peptides. Our own in-house proteomics software, which is continuously evolving, keeps track of all this information.

3. Photochemistry of peptide ions. As an alternative to conventional methods of collisional activation, we photodissociate ions in ion trap and in TOF mass spectrometers. Laser-induced photofragmentation is a novel high-energy activation process that provides unusual structural information that is of fundamental scientific interest and of practical significance for sequencing and analyzing peptides.

4. Protein structure and cellular fingerprinting. Enzymatic digestion of proteins allows us to identify sites at which proteins are mutated. Accessible sites on proteins are identified through chemical derivatizations. Mass spectra of bacteria enable different species and strains to be distinguished.

5. Novel time-of-flight instrumentation. Our research group has a history of developing novel scientific instrumentation. Through computer-assisted ion trajectory calculations, we attempt to optimize the sensitivity and resolution of mass spectrometers. MALDI TOF-TOF MS/MS instruments that feature a MALDI ion source in the first stage and ultraviolet laser-induced ion photofragmentation in the second are of particular interest.

Comparison of ion fragmentation patterns generated following photochemical and collisional peptide ion activation.

Publications

R.L. Beardsley, W.E. Running, J.P. Reilly, "Probing the structure of the Caulobacter crescentus ribosome with chemical labeling and mass spectrometry", J. Proteome Res. 5 , 2935-2946 (2006).

L. Zhang, W. Cui, M.S. Thompson, J.P. Reilly , "Structures of a-type ions formed in the 157 nm photodissociation of singly-charged peptide ions", J. Am. Soc. Mass Spectrom., 17 1315-1321 (2006).

J.A. Karty, W.E. Running, J.P. Reilly, "Two dimensional liquid phase separations of proteins using online fractionation and concentration between chromatographic dimensions", J. Chromatog. B 847, 103-113 (2007).

M.S. Thompson, W. Cui , J.P. Reilly, "Factors that impact the vacuum ultraviolet photofragmentation of peptide ions", J. Am. Society for Mass Spectrom., 18, 1439-1452 (2007).

W. Running, S. Ravipaty , J. Karty and J.P. Reilly, "A Top–down/bottom-up study of the ribosomal proteins of Caulobacter crescentus ", J. Proteome Res.6, 337-347 (2007).

Yi He and J.P. Reilly, "Does a charge tag really provide a fixed charge?, Angewandte Chemie., 120, 2497-2499 (2008).

A. Devakumar D.K. O'Dell, J. M. Walker and J.P. Reilly, "Structural analysis of leukotriene C4 isomers using collisional activation and VUV photodissociation", J. Am. Soc. Mass Spectrom., 19 14-26 (2008).

L. Zhang and J.P. Reilly, Use of 157 nm photodissociation to probe structures of y- and b-type ions produced in collision induced dissociation of peptide ions, J. Am. Soc. Mass Spectrom., 19 (5) 695-702 (2008).

A. Devakumar D.K. O’Dell, J. M. Walker and J.P. Reilly, “Structural analysis of leukotriene C4 isomers using collisional activation and VUV photodissociation”, J. Am. Soc. Mass Spectrom., 19 14-26 (2008).

A. Devakumar, Y. Mechref, P. Kang, M.V. Novotny and J.P. Reilly, “Identification of isomeric N-glycan structures by mass spectrometry with 157 nm laser-induced photofragmentation”, J. Am. Soc. Mass Spectrom. 19, 1027-1040 (2008).

W. Running and J.P. Reilly, “Ribosomal proteins of Deinococcus radiodurans: their solvent accessibility and reactivity”, J. Proteome Res., 8, 1228–1246, (2009).

J.P. Reilly, “Ultraviolet photofragmentation of biomolecular ions”, Mass Spectrometry Reviews. 28, 425-447 (2009).

L. Zhang and J.P. Reilly, “Extracting both peptide sequence and glycan structural information by 157 nm photodissociation of N-linked glycopeptides”, J. Proteome Res. 8, 734-743 (2009).

T-Y. Kim, J. Schwartz, and J.P. Reilly, “Development of a linear ion trap/orthogonal time-of-flight mass spectrometer for Time-Dependent Observation of Product Ions by Ultraviolet Photodissociation of Peptide Ions”, Analytical Chemistry, 81, 8809-8817, (2009).

L. Zhang, and J.P. Reilly, “Peptide Photodissociation with 157nm Light in a Commercial Tandem time-of-Flight Mass Spectrometer”, Analytical Chemistry, 81, 7829-7838 (2009).

T-Y. Kim and J.P. Reilly, “Time-Resolved Observation of Product Ions Generated by 157 nm Photodissociation of Singly Protonated Phosphopeptides”, J. Am. Soc. Mass Spectrom., 20, 2334-2341, (2009).

T-Y. Kim and J.P. Reilly, “Gas-Phase Conformation-Specific Photofragmentation of Proline-Containing Peptides”, J. Am. Soc. Mass Spectrom., 21, 1455-1465, (2010).

X. Liu and J.P. Reilly, “Correlating the chemical modification of Escherichia coli ribosomal proteins with crystal structure data”, Journal of Proteome Research, 8, 4466-4478 (2009).

L. Zhang, and J.P. Reilly, “Radical driven dissociation of odd-electron peptide radical ions produced in 157 nm photodissociation”, J. Am. Soc. Mass Spectrom. 20, 1378-1390 (2009).

M.A. Lauber, W.E. Running and J.P. Reilly, “B. subtilis ribosomal proteins:  structural homology, post-translational modifications, and genome sequencing errors”, J. Proteome Res.8, 4193–4206 (2009).

R. Parthasarathi, J.P. Reilly and K. Raghavachari, “New Insights into UV Photodissociation of Peptides”, Journal of the American Chemical Society, 132, 1606-1610 (2010).

L. Zhang and J.P. Reilly, “Peptide De novo Sequencing using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer”, Analytical Chemistry, 82, 898-908 (2010).

S. Ravipaty and J. Reilly, “Comprehensive Characterization of Methicillin-Resistant Staphylococcus aureus COL Secretome by Two-Dimensional Liquid Chromatography and Mass Spectrometry”, Molecular and Cellular Proteomics, 9, 1898-1919, (2010).

L. Zhang and J.P. Reilly, “De Novo Sequencing of Tryptic Peptides Derived from Deinococcus radiodurans Ribosomal Proteins Using 157 nm Photodissociation MALDI TOF-TOF Mass Spectrometry”, Journal of Proteome Research, 9, 3025-3034, (2010).

W. Running and J.P. Reilly, “Variation of the Chemical Reactivity of Thermus thermophilus HB8 Ribosomal Proteins as a function of pH”, Proteomics, 10, 3669-3687, (2010).

M. A. Lauber and J.P. Reilly, “A Novel Amidinating Cross-linker for Facilitating Analyses of Protein Structures and Interactions”, Analytical Chemistry, 82, 7736-7743, (2010).

B. C. Bohrer, Y. F. Li, J. P. Reilly, D. E. Clemmer, R. D. DiMarchi, P. Radivojac, H. Tang, and R. J. Arnold, “Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics”, Analytical Chemistry, 82, 6559-6568, (2010).

X. Liu, Y.F. Li, B.C. Bohrer, R.J. Arnold, P. Radivojac, H. Tang, J.P. Reilly, “Investigation of VUV photodissociation propensities using peptide libraries”, International Journal of Mass Spectrometry, 308, 142-154, (2011).

M. Lauber and J.P. Reilly, “Structural Analysis of a Prokaryotic Ribosome Using a Novel Amidinating Cross-Linker and Mass Spectrometry”, Journal of Proteome Research, 10, 3604-3616, (2011).

Y. He, J.F. Poehlman, A.W. Alexander, K. Boraas, J.P. Reilly, “One hundred anode microchannel plate ion detector”, Review of Scientific Instruments, 82, 08516, (2011).

Awards

• Max-Planck-Gesellschaft Zur Forderung Der Wissenschaften E.V., 1978-79
• Camille and Henry Dreyfus Grant for Newly Appointed Young Faculty, 1979
• Alfred P. Sloan Research Fellow, 1982
• Camille and Henry Dreyfus Teacher-Scholar Award, 1983
• Indiana University Teaching Excellence Recognition Award, 1998 and 1999

Highlights