Biomedical Engineering Reference
In-Depth Information
the peak position and intensity assignments and occur in addition to the
instrument precision. A peak detection procedure that leads to a low peak
position condence level would degrade the instrument performance that
researchers spent vast amounts of money and eort to improve.
When a peak is detected in a spectrum and compared with a database,
it is very rare to nd an exact match. It is almost certain that a search will
return a list of possible chemical IDs around the detected peak. Knowing the
position uncertainty will help us to determine how many possible chemical
IDs we should seriously consider. The position uncertainty would also help
to determine whether peaks that appear at slightly dierent positions in
dierent spectra are in fact the same, which is a crucial step in disease
associated biomarker discovery where comparison among a large number of
spectra is involved.
To summarize, what we want is an automated peak detection procedure
which gives best estimates of peak positions and peak intensities along with
their uncertainty estimates.
2. Methodology
2.1. Understanding TOF-MS
Since the goal here is to develop an algorithm that detects peaks in a TOF-
MS spectrum accurately and eciently, it is important to understand the
nature of mass spectrometry.
Mass spectrometry was started by J. J. Thomson, Physics Nobel laure-
ate of 1906, the discoverer of the electron. Since then, mass spectrometry
has become one the most useful tools in scientic research. A mass spec-
trometer dierentiates dierent molecular/atomic ions, which are generated
from the sample under investigation, according to their mass-to-charge
ratio (m=z). It can also give information about the abundance of each
species in the sample.
Roughly speaking, a mass spectrometer consists of three important com-
ponents: ion source, mass analyzer and ion detector. The ion source gener-
ates ions from the sample; the mass analyzer separates ions based on their
mass-to-charge ratio; the detector records the separated ions.
\Time-of-Flight" refers to the way that ions are separated, i.e., the
mass analyzer. The concept of a TOF mass analyzer is quite simple. Ions
start with the same kinetic energy, e.g., after falling through a xed elec-
trostatic eld , y through a eld-free tube, usually in vacuum, towards
an ion detector at the end of the tube. It is easily shown that the time that
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