Background:

• 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

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.

Selected Publications:

J.P. Reilly, “Laser Ionization Tutorial” in Encyclopedia of Mass Spectrometry, Vol. 6, (edited by Michael L. Gross), Elsevier Publishing, (2006).

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).

H. Tang, R. J. Arnold, P. Alves, Z. Xun, D.E. Clemmer, M.V. Novotny, Reilly, J. P.; P. Radivojac, “A computational approach toward label-free protein quantification using predicted peptide detectability” Bioinformatics, 22 (14), e481-e488 (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).

A. Devakumar, Y. Mechref, P. Kang, M.V. Novotny, J.P. Reilly, “Laser-Induced photofragmentation of neutral and acidic glycans inside an ion-trap mass spectrometer”, Rapid Commun. Mass Spectrom. 21, 1452-1460 (2007).

X. Liu, W.C. Broshears and J. P. Reilly, “Probing the structure and activity of trypsin with amidination”, Anal. Biochem., 367, 13-19 (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).

R. J. Arnold, William Running and J.P. Reilly, “Analysis of Methylation, Acetylation and other Modifications in Bacterial Ribosomal Proteins” Chap. 11, pgs, 151-161, Post-translational Modifications of Proteins, Tools for Functional Proteomics, 2nd Edition , Kannicht, Christoph (Ed.), Methods in Molecular Biology, Vol 446 (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).