Proteomics 2

Question 1

What is the concept of P4?

Answer 1

the proposition that healthcare is evolving from reactive disease care to care that is:
-predictive
-personalized
-preventive
-participatory

Question 2

What are the benefits of the P4 medicine?

Answer 2

provide more cost-effective disease care
reduce the incidence of disease
replicate the innovation cycle of systems medicine on a large scale, as both disease care and wellness support are integrated within a discovery science to create a learning healthcare system

Question 3

What is systems biology?

Answer 3

the study of biological systems as collections of networks at multiple levels, ranging from the molecular level, through cells, tissues and organisms, to the population level

Question 4

What is the purpose of systems biology?

Answer 4

decode the biological complexity of disease

Question 5

What is systems medicine?

Answer 5

medical application of systems biology, mathematical modelling and systems theory
in effect “omics” approaches are becoming integral to precision medicine

Question 6

What is “omics”?

Answer 6

the study of x and their interactions and how they influence eachother

Question 7

Pharmacometabolomics is currently classified under pharmacoproteomics, how should it be classified?

Answer 7

should stand alone
-fastest growing field

Question 8

What is pharmacoproteomics?

Answer 8

pharmacoproteomics deals with the changes in the abundance of the proteins caused by the administration of the medications, and therefore examines at the protein level “what the drug does to the body”, including the side effects
-can be viewed as the molecular pharmacodynamics of the “omics era”

Question 9

What does “omics” stand for in the word proteomics?

Answer 9

sub-typing of patients based on the basis of protein analysis
matching a particular target-based therapy to a particular marker in a subgroup of patients
providing optimal detection of disease at an early stage for prevention and early intervention
safety of drugs

Question 10

Why is pharmacoproteomics a more functional representation of patient-to-patient variation that that provided by genotyping?

Answer 10

captures post-translational modifications
splice variation: a single gene can code for multiple proteins, prior to mRNA translation, by the differential inclusion or exclusion of regions of pre-mRNA
protein coding genes are estimated in the range of 19,000-21,000 while the actual number of proteins can reach probably millions derived from these genes

Question 11

What does proteomics allow for understanding of?

Answer 11

allows understanding of diseases at the molecular level
-most human diseases are multifactorial
-proteomics reveals a more dynamic picture of the disease progress

Question 12

What are the key technologies used in proteomics to identify disease targets?

Answer 12

gel electrophoresis
chromatography
immunoassays
mass spectrometry

Question 13

What is the purpose of gel electrophoresis?

Answer 13

isolation
identification
quantification

Question 14

What is the purpose of chromatography?

Answer 14

isolation
identification
quantification

Question 15

What is the purpose of immunoassays?

Answer 15

identification
quantification

Question 16

What is the purpose of mass spectrometry?

Answer 16

identification
quantification

Question 17

What is the gel used in gel electrophoresis?

Answer 17

SDS-PAGE

Question 18

Provide a brief overview of gel electrophoresis.

Answer 18

protein samples and marker loaded in vertical SDS-PAGE system
direction of migration of samples in vertical SDS-PAGE system
stain and compare to control

Question 19

What technology does gel electrophoresis depend upon for visualization and measurement?

Answer 19

protein-antibody interactions
-primary and secondary antibodies

Question 20

What is a Western Blot?

Answer 20

gel pattern from gel electrophoresis can be plotted on a cellules membrane for visualization and quantification

Question 21

How is actual identification and quantification of gel electrophoresis analysis done?

Answer 21

LC-MS analysis
-top down proteomics or bottom up/shotgun proteomics

Question 22

True or false: LC-MS has been advanced significantly that it can be applied at whole sample without electrophoresis

Answer 22

true

Question 23

What is immunoassay?

Answer 23

highly selective bioanalytical method that measures the presence or concentration of analytes ranging from small molecules to macromolecules through the use of an antibody or an antigen as a biorecognition agent
-NO isolation involved

Question 24

What is chromatography?

Answer 24

analytes are separated based on their partition coefficients between two different liquids (stationary & mobile phases)

Question 25

What is mass spectrometry?

Answer 25

a technique in which gas phase ions are separated and detected according to their mass-to-charge ratio (m/z)

Question 26

Which technology used in proteomics is the most complex?

Answer 26

mass spectrometry

Question 27

What are the two fundamental questions answered by mass spectrometry?

Answer 27

what and how much?

Question 28

Provide a simplified description of how mass spectrometry works.

Answer 28

inlet –> ion source –> vacuum & analyzer –> detector

Question 29

What is the column of choice for proteomics analysis?

Answer 29

C8

Question 30

What is toxicoproteomics?

Answer 30

seeks to determine how chemical exposure modifies proteins or protein expression as a form of preclinical risk assessment
identified protein changes may translate into new biomarkers that may be used to monitor treated patients for signatures of chemical toxicity
studies extend beyond the application of drug development and may be used to assess the toxic effects of other chemical agents