Up until recently, most mass spectrometry biomarker discovery strategy focused on small peptide fragments
ignoring the post translational landscape of larger peptides and intact proteins. Top down proteomics
analyzes the intact protein and all its post translational modification in one single run. Here we describe an
extension to a new top-down proteomics algorithm developed at Merck called MAR. The software runs on
Linux clusters, relies only on a predefined list of ?differential? modifications (e.g., phosphorylation) and a
FASTA-formatted protein database, and is not constrained to full-length proteins for identification. The added
functionality to the recently published work elaborates on techniques that locate post-translational modifications
within high scoring candidate polypeptide matches. These candidates are then further scored to determine the
location of the modified residue. Since the publication, the software has been re-written several times and is
now equipped to handle many simultaneous PTMs within a single polypeptide and determine each of their
residue locations. The application of these new developments for protein id may be very useful in areas such as
neuroproteomics and neurology.
Ray Fyhr has an AB degree from Colgate University and an MS degree in Computer Science from New York Institute of Technology.
With over 30 years of professional experience as a software developer and business analyst, his career has traversed many
industries including pharmaceutical, communications, financial, transportation, manufacturing, and operations research. In 2004,
Mr. Fyhr joined Merck supporting the information technology needs of the Proteomics department. This included a customized
LIMS deployment and other lab automation endeavors involving Elucidator and HPC. Of particular interest to Ray is developing
software which solves complex research problems. Now he is involved with implementing new algorithms for Top-Down Proteomics
and other types of biomarker analyses.
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