1. wileyonlinelibrary.com/journal/jms
Journal of
MASS
Volume 47 Number 4
April 2012 SPECTROMETRY
Special Feature: Tutorial
(wileyonlinelibrary.com) DOI: 10.1002/jms.3002
GenoMass software: a tool based on electrospray ionization tandem mass spectrometry
for characterization and sequencing of oligonucleotide adduct
Vaneet K Sharma, James Glick, Qing Liao, Chang Shen and Paul Vouros
Page 490–501
Today mass spectrometry plays a prime role for structural analyses in the
field of proteomics. This is in large part due to significant development of
methodologies for the interpretation of the vast amount of MS/MS data
acquired and the possibility to search this information in protein databases.
Such approaches and methods are emerging for structural analyses in the
field of genomic. In this special feature article, Paul Vouros and colleagues
present the potential of new in-house developed software named GenoMass,
capable of analyzing MS/MS sequencing data of oligonucleotides to identify
the exact location of potential adducts. The analysis of DNA adducts is of
prime importance in our quest to understand DNA damage and the advent
of related diseases. Paul Vouros is Professor of Chemistry and Chemical
Biology at Northeastern University (Boston, MA). The main research focus of
his laboratory is the development and applications of capillary hyphenated
MS/MS techniques for the analysis of biomarkers indicative of exposure to
environmental carcinogens or of other biological processes.
Authors’ biographies
Professor Paul Vouros is a graduate of Wesleyan University, James Glick obtained his Ph.D. in analytical chemistry at
Middletown, CT (1961) and received his Ph.D. in Analytical Northeastern University in the lab of Professor Paul Vouros using
Chemistry from the Massachusetts Institute of Technology in LC-MS for the quantitative analysis of genomic damage from
1965 under the direction of Professor Klaus Biemann. After a brief foodborne carcinogens. After a brief stint as a postdoctoral fellow
period in industry, he joined the Institute for Lipid Research at in the Barnett Institute of Chemical and Biological Analysis, he
Baylor College of Medicine as an Assistant Professor between is now the Director of the Core Mass Spectrometry facility at
1968 and 1974 where he worked on a variety of bioanalytical Northeastern University. In addition to his work in small molecule
problems using the then still developing technologies of and oligonucleotide LC-MS, he teaches Undergraduate level courses
GC-MS in the laboratory of Professor Evan Horning. He has been in Quantitative Analytical Chemistry and Instrumental Analysis.
at Northeastern University since 1974 where he is currently
Professor of Chemistry and Senior Faculty Fellow in the Barnett
Institute. For the past several years a major area of his work has
involved the sensitive development of methodology based on Qing Liao obtained B.S. and M.S. in analytical chemistry from
capillary LC-MS for the analysis of DNA adducts. The present the University of Mississippi. She earned her Ph.D. in mass
publication represents an expansion of these studies toward spectrometry from Northeastern University. Dr. Liao worked for
the characterization of adduct formation in the context of Pharmacopeia and Pfizer before she became the manager of the
base sequence. Mass Spectrometry Facility of Harvard University and remained
there for seven years. She is currently the Chief Scientific Officer at
Shenitech LLC.
Vaneet Kumar Sharma is a Graduate Research Assistant at
Northeastern University, Department of Chemistry and Chemical
Biology and the Barnett Institute of Chemical and Biological
Analysis. He received his Bachelor (B.Sc. (Hons. school), 2001) Chang Shen, is a 25-year veteran of electrical engineer and computer
and Masters (M.Sc. (Hons. school), 2003) degrees from the Guru specialist. He received his Ph.D. from Swiss Federal Institute of
Nanak Dev University, Amritsar, India. He holds another Masters Technology – Lausanne (EPFL). He worked in process instrumentation
in Chemistry (M.S., 2008) from the University of Connecticut, with industry, semiconductor industry, telecommunication industry as
an emphasis in nanotechnology. In 2008, he joined Northeastern well as biotechnology industry as a Principal Engineer. He is the
University for his Ph.D. in the lab of Professor Paul Vouros. founder and currently the President of Shenitech LLC in Acton, MA,
developing cutting-edge products for flow and energy measurement.
His research focus involves the use of monolithic columns
applied to genotoxin-modified oligonucleotides and the
development of software for the identification and sequencing of
modified oligonucleotides.