Proteomics Flashcards
What is proteomics
The study of a proteome
The main aim is quantification
How many essential amino acids
20
Why use proteomic technologies
To identify and wuantify overall proteins better than genomics
What are the challenges with studying proteomics (6)
Proteins are complex and dynamic
Low abundance
Quantification
Protein protein interaction
Data analysis
Post translational modifications
How to overcome challenges
By using fractionation and seperation methods to seperate into simpler fractions
Immunodepltion to remove abundant proteins
What is mass spec
Measuring accurate molecular mass
What is CID
Collision induced dissociation
Fragmentation technique for ions most selected
What quantitative technologies are there (3)
Label free- measures peptide ion intensity
Chemical mass tagging (TMT)
In vitro metabolic labelling SILA
What os metabolomics
The study of chemical processes involving metabolites
Provides a snapchot of cellular phenotype
What applications are used in cancer research (5)
Cancer biomarker discovery
Targegted Ms based assay
Functional characterisation
P-P interactions
Identification of PTM
What is ELISA
Enzyme linked immunosorbent assay
A capture antibody, second antibody + 3rd enzyme linked HRP antibody
Detects antibodies on the blood
What is the Proteome Human atlas
Large scale IHC
3 parts of a mass analyser
Ion source
Mass analyser
Detector
Types of mass analyser
Time of flight, quadruple, ion trap, orbitrap
Ionisation methods
MALDI
Electrospray ionisation
Ideal sample for MS
Can change to gaseous state, ionisable, stable and can be digested by a protease ( trypsin)
Protein seperation methods
Electrophoresis:
GEL electrophoresis- size and charge
Free flow capillary electrophoresis- based on charge only
liquid chromatography:
Size exclusion- molecular size / retention time
Ion exchange- charge
Reverse phase LC- hydrophobic interaction
Affinity- antigen- antigen ( binding properties)
What technique is metabolomics validated by?
ELISA
protein arrays and large scale IHC
Methods to improve proteomic coverage
Fractionation and enrichment methods
