2018

The Development Process

and Future Prospect of
Proteomics
• Proteomics has become one of the most
effective methods for molecular markers
of disease and drug targets. In cancer,
Alzheimer's disease and other major
human diseases clinical diagnosis and
treatment, proteome technology also has
a very attractive prospect. Recently , there
are new breakthroughs in the
development of Proteomics, and we have
prepared several materials for you.
• Professor John R . Yates, an international
famous proteomic expert from the Scripps
Institute in the United States of America,
was invited to attend the 5th Asia-Pacific
Mass Spectrometry Conference in Beijing
to report. In the first half of his report ,
Prof. Yates described the development
process of proteomics and the direction in
the future.
The Evolution of
shotgun proteomics

• The development of proteomics

is together with the development
of Protein MALDI-TOF
technology. Over the past 100
years, mass spectrometry has
grown exponentially. This
progress can be attributed in part
to innovations in the mechanical,
electronic and computer
industries. But there have been
occasional disruptive
breakthroughs. It is possible the
fundamental cause for the
development of mass
spectrometry. It is these
subversive breakthroughs that
make large-scale protein analysis
or proteomics possible.
 Identification of protein function

Another important task of proteomics is to

identify the function of proteins encoded in a
gene sequence. Shotgun proteome
technology allows people to quickly acquire
information through some new strategies,
including methods based on concept of "
linked crime "; enrichment and
reidentification of protein based on activity;
whole cell or organelle analysis, etc.
 Regulation of biological system

The molecular structure to modify proteins is very various. These modifications are of a significant regulatory
function, and some are merely altering the chemical properties of the protein without significant regulatory
functions. Modifications with regulatory functions are usually reversible except for proteolytic process.
Protein Quantification

The invention of stabe isotope protein

standard gives rise to the idea of molecular
quantification using mass spectrometry data.
Furthermore, for in vivo metabolic studies
( determining the importance of amino acids ),
the SIL is also an essential element of
quantitative mass spectrometry.
In vivo labelling of the whole animal

Introducing stable isotope label into the human and

animal body is for measuring the final metabolic product
of the molecule. Metabolic analysis is achieved by tracing
isotope labeled amino acids and isotope ratio mass
spectrometry techniques. Metabolic stability isotope
labeling is a very powerful method for studying animal
biology. The overall animal labeling enables research
topics to involve more complex systems than cell lines
and can better reflect the biological mechanism of
organisms. Stable isotope labeling of animal bodies
allows people to use tissues or organs for disease
research. In addition, tissues and organs are, in fact, a
collection of many different cell types, and ultimately, the
purpose of the study is to understand how the confluence
of these cells exerts their function.
The paradox of quantitation and identification
• For the shotgun proteomics, quantitation and identification strategies will produce a
paradox. In a full mode, the identification of proteins in a complex system requires rapid
scanning instruments and efficient chromatography to maximize the capacity of MSMS.
The instrument should be able to quickly collect a peptide data, and then move on to the
next new peptide. In order to accurately measure the difference between the two forms,
the peptide segment quantification needs to collect enough data points. The "speed" and
"lasting", these two paradoxes led to a compromise on the quality of quantitative data,
because the detection limit for peptide identification is more than the limit of quantification.
Another problem is measuring the presence or absence in the quantitative experiments.
In order to further calculate peptide measurement results, most of the software tools
require the presence of the peptide segments marked by heavy and light isotopes. When
the ratio of different labeled peptides exceeds 10:1, the quantitative efficiency begins to
decline, and some major changes may be missed. Some unlabeled methods, such as
spectral counting, can better determine a number of large changes, but their accuracy is
not as good as that of labeled method.
Future prospect
Protein complexes represent a higher structure in the cell. Determining how protein
isoforms or modified forms influence the protein complex function or activity will be
the next step of work. At the same time, we also look forward to the progress of mass
spectrometry by science and technology as well as the intense commercial
competition. In order to provide a better tool for proteomics, the scanning speed and
sensitivity of the mass spectrometer will be further improved.
Link:
https://medium.com/@contact_28268/the-development-
process-and-future-prospect-of-proteomics-2254a0fd1ccb
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