Princeton Docket #
11-2630-1
Researchers in the
department of molecular biology Princeton University have developed a method
that directly incorporates chromatographic relationships between modified forms
into post-translational modifications (PTMs) identification and quantitation
problems. In particular, this method establishes a priori relative
elution relationships between modified forms of the same peptide with respect to
the type of chromatography (e.g., reversed phase) used to separate the sample
mixture. These relationships are then built into the model, which is formulated
as an optimization problem in order to simultaneously consider the retention
time and m/z dimensions when solving the PTM identification and quantitation
problem. Thus, just solving one optimization model, which is more reflective of
the large-scale and complementary LC-MS/MS data structure, simultaneously
identifies and quantifies all modified forms of the same peptide.
Furthermore, the method is able to deconvolve co-eluting isobaric peptides
present in mixed tandem MS (i.e., spectra containing the fragment ions of more
than one modified form) and make accurate and robust identifications to
incomplete tandem MS.
Advantages:
- High-quality and
comprehensive unbiased, quantitative readouts of all modifications present on
histone proteins
- Direct
integration of chromatography information for the identification of modified
peptides
- Ability to
interpret `mixed¿ tandem mass spectra resulting from the co-fragmentation of
co-eluting isobaric modified forms
Applications:
- Study of
post-translational modifications on histone proteins
- Drug discovery ¿
target identification
- Study of
eukaryotic gene regulation and chromatin-related processes
Background:
Existing
computational methods for quantitating peptide post-translational modifications
(PTMs) using liquid chromatography tandem mass spectrometry (LC-MS/MS) data must
decouple this large-scale data into smaller and sequential subproblems for
tractability purposes. This type of approach loses important connectivity
between modified species with regards to their physicochemical properties and is
susceptible to the propagation of error between subproblems. In particular,
modified forms are independently identified using isolated tandem mass spectra
without considering their temporal relationship to other modified forms of the
same peptide sequence. Furthermore, lower abundance modified forms for which no
tandem MS are available (due to dynamic range limitations of the MS) or isobaric
and co-eluting modified forms are not detected by such approaches.
Inventors:
Benjamin A Garcia
Benjamin Garcia is an
Assistant Professor in the Department of Molecular Biology. His research is
focused on developing novel mass spectrometry based proteomic methodologies for
quantitatively characterizing changes in protein expression and
post-translational modification state within a given proteome during significant
biological events or in response to external perturbation. Garcia¿s goal is to
utilize large-scale proteomic data to improve our understanding of biological
processes at the molecular level. Histone modifications have emerged as a key
mechanism of epigenetic inheritance. Utilization of advanced proteomic
technology in chromatin biology will enhance investigations of histone
modifications to a much higher scale.
Garcia received his
B.S. from the University of California, Davis and a Ph.D from the University of
Virginia, both in chemistry. Professor Garcia holds numerous awards of which
most recent include the New Jersey American Chemical Society Early Career Award
in Mass Spectrometry 2011, NIH Director¿s New Innovator Award 2010-2015, and the
NSF Faculty Early CAREER Award 2010-2015.
Peter A. DiMaggio,
Jr.
Peter DiMaggio is a
post-doctoral research fellow in the Department of Molecular Biology. His
research is centered upon the development of mathematically rigorous
computational platforms for the characterization of targeted protein systems
using LC-MS/MS data. DiMaggio received his B.S. from the University of Rhode
Island and his Ph.D. from Princeton University, both in chemical engineering. He
is a recipient of the Jacobus Honorific Fellowship, which is the highest honor
conferred by the Graduate School at Princeton, and the NIH/NRSA Ruth L.
Kirschstein Postdoctoral Fellowship.
Intellectual property
and technology status:
Patent pending
The method has been
rigorously tested and benchmarked against manually curated data. Industrial
collaborators and licensees are sought to further establish this methodology.
Contacts:
Laurie Tzodikov
Princeton University
Office of Technology Licensing ¿ (609) 258-7256¿ tzodikov@princeton.edu
Princeton docket #
11-2630