Biomedical Engineering Reference
In-Depth Information
proteins, instead of DNA, give more complete information related to cell
function. Hence, proteins, the nal product of genes, are receiving increased
attention and a new eld, proteomics, which focuses on protein characteri-
zation, protein identication and protein function, has emerged.
Although two-dimensional gel electrophoresis and amino acid sequenc-
ing, which have been in use for decades, retain their important roles in bio-
chemical analysis, recent developments in mass spectrometry (MS) have
now made it an additional analytical tool in proteome research
1;2
. Mass
spectrometry can give accurate mass \ngerprints" which, in conjunction
with protein database searching, can rapidly provide information about
protein identication, protein function and protein post-translational mod-
ication (i.e., modications after the polypeptide is synthesized).
In protein identication, matrix assisted laser desorption/ionization
mass spectrometry (MALDI-MS) and electrospray ionization mass spec-
trometry (ESI-MS) are often used because they can ionize large biological
molecules `softly' without breaking most of them into smaller pieces.
To identify proteins, proteins are often digested by a protease such as
trypsin into peptides and mass ngerprints of the resulting peptides are
often measured by MALDI. The mass ngerprints of these peptides are
then compared with tryptic peptide masses that are theoretically gener-
ated from protein sequence databases using programs such as Sequest or
Mascot. These programs use sophisticated scoring algorithms to evaluate
the degree of match between the theoretically predicted mass spectra and
the experimentally generated spectra.
The high throughput, high sensitivity and quantitative analysis of mass
spectrometry make it possible to analyze hundreds of analytes over a large
mass range simultaneously even if the sample volume is small. If a biologi-
cal uid, such as blood, is measured, a protein \prole" may be developed.
This leads to the potential for nding biomarkers that are overexpressed
or underexpressed or modied. Such biomarkers can then be used to dif-
ferentiate pathological states (disease) from normal states or to assess and
guide drug treatments. If desired, the discovered biomarker can be chemi-
cally extracted for further analysis. Progress has been made with this line
of cancer research as summarized in [3, 4, 5, 6, 7, 8].
All information that mass spectrometry provides is encoded by peaks
that occur at dierent masses with various intensities in the spectrum.
The number of peaks present varies with the sample under investigation
and the type of mass spectrometer used. If biological or organic samples
are investigated, the peak number can easily rise to a few hundred. In
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