Omics 3.

Proteomics
- Study of proteins to provide a
comprehensive view of structure,
function and regulation within a cell
Omics Collective technology used to study system or organism
various molecules - Proteome: set of all proteins
expressed in a given set of genes

1. Genomics
- comprehensive analysis of DNA
structure and Function
- Genome: total DNA complement
Areas of Genomics
1. Structural Genomics structure of the
genomes
2. Comparative Genomics comparison of
genomes
3. Functional Genomics genome function
model
4. Pharmacogenomics how genes influence
drug response
2. Transcriptomics
- Study of mRNA or transcript
- Global and quantitative analysis of
gene expression under defined set of
conditions
- Transcriptome: total mRNA of a cell
or organism
4. Metabolomics
- Study of global metabolite profiles in
a system under given set of condition
- Metabolic Profiling
- Metabolome: total quantitative
collection of low molecular weight
compounds (metabolites) that
precipitate in metabolic reaction
- Primary metabolites: indispensable
for growth
Integrated Approach
no ome is alone and it must not be forgotten
that cell function is dictated by tightly controlled
interactions between the omes.
Integrome Analysis
- Network map of the interactome
together with a list of mutliomics data
that allows analysis of cancer cells
and normal cells, effect of treatment,
etc.

- multiomics data and interactome

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 Multiomics Data genes,
transcript, metabolite and protein
specific information
Interactome network of data
that are obtained based on direct
interactions between molecules
General Flow of Mass Spectrometry

The Omics Experiment

Process flow for
1. Experimental Design Consideration gene expression
- Use of suitable biological samples microarray
Depends on the objective of experiment
the experiment
Biomarker discovery
- Technical / analytical variation
Relative standard deviation of
a specific experimental
technique
Needs to be validated
- Biological variation
Very large variation in humans
Meta data: data about data
Match comparison groups
strongly to ensure that
changes are not due to
confounding factors

2. Analytic Techniques
- Sample preparation is imperative
and should be standardized and
reproducible
- Mass spectrometry
Commonly used method
Ions are created from neutral
proteins, peptides or
metabolites, which are then
separated according to their
mass-to-charge ratio (m/z)
and detected to create a
mass spectrum

Simplified schematic workflow for proteomics

experiments
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 GC: Gas Chromatography
LC: Liquid Chromatography
MALDI/TOF: Matrix Assisted Laser
Desorption/ Ionization / Time of Flight
MCP: Microchannel Plate

3. Data Analysis
- Find data patterns that provide useful
biological information
- Bioinformatics
- Statistics
Data validation

Next Generation Technologies for

Multiomics Approaches
1. Genomics
- Next Generation Sequencing: After
Sanger Sequencing Method
- Whole genome sequencing: used to
detect mutations by sequencing the
whole genome and used for
analyzing exon regions
- Determines somatic mutations such
as SNPs and InDel

Simplified schematic workflow for

metabolomics experiments

Other Technologies:

CE: Capillary Electrophoresis

CI: Chemical Ionization
EI: Electron Impact Ionization
ESI: Electrospray Ionization;
FTICR: Fourier Transform Ion Cyclotron
Resonance Next Generation Sequencers

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 - Used for mRNAs or long noncoding
RNAs
- Analysis of gene expression or
detection of fusion genes and splice
variants
- Studies unique patterns
- Microarrays:
Gene expression
Relative quantification of
expression
Computed
- RNA sequencing
Absolute quantification of
expression
Detecting unknown
transcription products

Comparison of Sequencing Technologies

2. Transcriptomics
- RNA sequencing

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 Applications of Omics

1. Biomarker Discovery
- Inflammatory lung disease
- Reproductive Medicine

2. Autism Spectrum Disorders

3. Ageing

4. Precision Medicine
- Integrate genetic and environmental
information

3. Metabolomics
5. Clinical Medicine
Non Targeted Metabolome
Unknown metabolite
and determine its
relative amount
Targeted Metabolome
Focused on a specific
metabolic pathway
Comparison for Major
Metabolomes Method
Nuclear Magnetic
Resonance
Gas Chromatography
Mass Spectrometry
Liquid Chromatography
Mass Spectrometry
Capillary
Electrophoresis Mass
Spectrometry

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