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:

R. L. Beardsley and J.P. Reilly, "Optimization of guanidination procedures for MALDI mass mapping", Anal. Chem. 74, 1884-1890 (2002).

M.M.E. Ireland, J.A. Karty, J.P. Reilly and Y.V. Brun, "Proteomic analysis of the Caulobacter crescentus stalk indicates competence for nutrient uptake", Mol. Microbiol. 45, 1029-1041 (2002).

J.A. Karty, M.M.E. Ireland, Y.V. Brun and J.P. Reilly, "Defining absolute confidence limits in the identification of Caulobacter proteins by peptide mass mapping", J. Proteome Res. 1, 325-335 (2002).

W.A. Harris and J.P. Reilly, "On-probe digestion of bacterial proteins for MALDI-MS", Anal. Chem. 74, 4410-4416 (2002).

A.J. Moad, L.J. Klein, D.G. Peters, J.A. Karty, J.P. Reilly, "Catalytic reduction of ethyl chloroacetate by cobalt(I) salophen electrogenerated at vitreous carbon cathodes", J. Electroanal. Chem. 531, 163-169 (2002).

J.A. Karty, M.M.E. Ireland, Y.V. Brun and J.P. Reilly, "Artifacts and unassigned masses encountered in peptide mass mapping", J. Chromatogr. B, 782, 363-383 (2002).

W.A. Harris, D.J. Janecki, and J.P. Reilly, "Use of matrix clusters and trypsin autolysis fragments as mass calibrants in matrix-assisted laser/desorption ionization time-of-flight mass spectrometry", Rapid Commun. Mass Spectrom. 16, 1714-1722 (2002).

R.L. Beardsley and J.P. Reilly, "Quantitation using enhanced signal tags: a technique for comparative proteomics", J. Proteome Res. 2, 15-21 (2003).

R. M Alvey, J.A. Karty, E. Roos, J.P. Reilly, and D. M. Kehoe, "pebAB, the operon encoding 15,16-dihydrobiliverdin oxidoreductase and PEB oxidoreductase, is coordinately regulated with cpeBA during complementary chromatic adaptation in Fremyella diplosiphon", Plant Cell, 15, 2448-2463 (2003).

R.L. Beardsley and J.P. Reilly, "Fragmentation of amidinated peptide ions", J. Am. Soc. Mass Spectrom., 15, 158-167 (2004).

J.A. Karty, T-Y. Kim, J.P. Reilly, "Utility of chemical derivatization schemes for peptide mass fingerprinting" in Sample Preparation for Hyphenated Analytical Techniques, edited by J.A. Rosenfeld, (Blackwell Publishing, CRC Press, Oxford, UK) pp. 52-79 (2004).

D.M. Goken, D.G. Peters, J.A. Karty, J.P. Reilly, "Alkylation of [2.2'-([2,2'-bipyridine]-6,6'-diyl)bis[phenolato]-N,N'O,O']nickel(II) during catalytic reduction of 1-iodooctane", J. Electroanal. Chem., 564, 123-132 (2004).

M. S. Thompson W. Cui, and J.P. Reilly,"Fragmentation of singly-charged peptide ions by photodissociation at λ = 157 nm", Angewantde Chem. 116, 4895-4898 (2004).

J.D. Persinger, J.L. Hayes, L.J. Klein, D.G. Peters, J.A. Karty, J.P. Reilly, "Catalytic reduction of 1,1,2-trichloro-1,2,2-trifluoroethane (CFC-113) by cobalt(I) salen electrogenerated at vitreous carbon cathodes", J. Electroanal. Chem. 568, 157-165 (2004).

D. Janecki and J.P. Reilly, "Photoimmobilization of proteins for affinity capture with MALDI TOF MS analysis", Anal. Chem. 76. 6643-6650 (2004).

T.J. Tegeler, Y. Mechref, K. Boraas, J.P. Reilly, M.V. Novotny, "Microdeposition device interfacing capillary electrochromatography and microcolumn liquid chromatography with matrix-assisted laser desorption/ionization mass spectrometry", Anal. Chem. 76, 6698-6706 (2004).

T-Y. Kim, Y.V. Brun, and J.P. Reilly, "Effects of tryptic peptide esterification in MALDI mass spectrometry", Anal. Chem.77, 4185-4193.

R.J. Arnold, J.A. Karty and J.P. Reilly, "Bacterial strain differentiation by mass spectrometry" (book chapter in Identification of Microorganisms by Mass Spectrometry, edited by Charles L. Wilkens (John Wiley and Sons), in press.

D. Janecki and J.P. Reilly, "Denaturation of metalloproteins with EDTA to facilitate enzymatic digestion and mass fingerprinting", Rapid Commun. in Mass Spectrom. 19, 1268-1272 (2005).

R.L. Beardsley, L.A. Sharon, and J.P. Reilly, "Peptide de novo sequencing facilitated by a dual labeling strategy" Anal. Chem. (in press).

W. Cui, M.S. Thompson and J.P. Reilly "Pathways of peptide ion fragmentation induced by vacuum ultraviolet light", J. Am. Soc. Mass Spectrom. 16, 1384-1398 (2005).

J.A. Karty and J.P. Reilly, "Application Note: Deamidation as a consequence of β-elimination of phosphopeptides", Anal. Chem. 77, 4673-4676 (2005).

T.-Y. Kim, M.S. Thompson and J.P. Reilly, "157nm photodissociation of peptides in a linear ion trap mass spectrometer", Rapid Comm. in Mass Spectrom. 19, 1657-1665 (2005).

A. Devakumar, M.S. Thompson and J.P. Reilly, "Fragmentation of Oligosaccharide Ions with 157 nm Vacuum Ultraviolet Light", Rapid Commun. in Mass Spectrom. 19, 2313-2320 (2005).