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E u r o S c i C o n c o n f e r e n c e o n
Protein, Proteomics and
Computational Biology
Biochemistry & Molecular Biology Journal
ISSN: 2471-8084
D e c e m b e r 0 6 - 0 7 , 2 0 1 8
Am s t e r d a m , N e t h e r l a n d s
Proteomics and Computational Biology 2018
Page 21
C
urrently, great interest is paid to the identification of "missing" proteins that
have not been detected in any biological material at the protein level (PE1).
Using the UPS1 and UPS2 Sigma Aldridge sets as the “gold standard”, we
characterizedmass spectrometric approaches from the point of view of sensitivity
(Sn), specificity (Sp) and accuracy (Ac). This sets consists of 48 high purity human
proteins without SAP or PTM. UPS1 set consists of the same 48 proteins at 5
pmols each, in UPS2 proteins were unified into five groups in accordance with
their molar concentration, ranging from 10-11 M to 10-6 M. Single peptides from
the ninety-two and ninety-six percent of all set proteins could be detected in a
pure solution of UPS2 and UPS1, respectively, by Selected reaction monitoring
with stable isotope-labeled standards (SRM SIS). We also found that in the
presence of a biological matrix such as
E.coli
extract or human blood plasma
(HBP), SRM SIS makes it possible to detect from 63% to 79% of proteins of the
UPS2 set (sensitivity), with the highest specificity (~100%) and an accuracy of
80%. To increase the sensitivity of shotgun and SRMSISmonitoring samples were
fractionating by RP using chromatography under alkaline condition (2D-LC_alk). It
is shown that this technique allows the SRM SIS to detect 98% of the the single
peptides from the proteins present in the pure solution of UPS2 (47 out of 48
proteins).When the extracts of
E-coli or P. Pastoris
are addedas biologicalmatrixes
to the UPS2, 46 and 45 out of 48 proteins (~95%) can be detected respectively.
The combination of the 2D-LC_alk SRM SIS and shotgun technologies allows to
increase the sensitivity up to 100% in case of the proteins of UPS2. The usage of
that technology can be a solution for identifying the so-called "missing" proteins
and, eventually, creating the deep proteome of a particular chromosome of tissue
or organs. Data in PASSEL PASS01192 and PRIDE PXD007643.
Biography
Professor, Scientific Advisor of Institute of Biomedical
Chemistry, Was born January 10, 1940, in Kashin, Kalinin
(Tver) region – scientist, biochemist. A.I. Archakov had
organized a scientific school to study molecular organization
and functioning of oxygenase cytochrome P450-containing
systems, molecular mechanisms of the structure and function
of membranes and biological oxidation. Under the guidance
of A. I. Archakov, the institute’s members have developed a
fundamentally new pharmaceutical composition “Phosphogliv”
with antiviral activity for the treatment of liver diseases of
various etiology. A.I. Archakov’s present-day/current areas
of expertise relate to research in the field of post-genomic
technologies, nanobiotechnologies, proteomics, development
of approaches to create personalized medicine of the future.
A.I. Archakov is the pioneer in the development of proteomics
in Russia. Currently, he is the international “Human proteome”
project coordinator in Russia/ the coordinator representing
Russia in the international “HP” project.
archakov@ibmh.msk.suThe Way to Deep Cover of Human Proteome
in Gene-centric Mode
Alexander I. Archakov, Ekaterina
V. Ilgisonis, Arthur T. Kopylov,
Andrey V. Lisitsa, Elena A. Ponomarenko,
Victor G. Zgoda
Institute of Biomedical Chemistry, RAS, Moscow, Russia
Alexander I et al., Biochem Mol biol J Volume:4
DOI: 10.21767/2471-8084-C5-020