Proteomics

Presented To
Rabia Saba
Presented By
Laraib Muneer
Roll no
BSBOTF16R22
University of Sargodha Sub Campus Bhakkar
 Contents
• Introduction
– Who coined this Term?
– Definition
• Types of Proteomics
– Interaction Proteomics
– Expression Proteomics
• A mass spectrometry workflow for measuring
protein turnover rates in vivo(Most Recent)
• Tools of Proteomics
• Post Translational Modification
• Techniques of Proteomics
• Applications of Proteomics
 Introduction
• The term proteomics was coined by Mark
wilkins and colleagues
• Proteomics is the study of composition,
structure, function and interaction of the
proteins directing the activities of each
living cell
• Many types of information cannot be
obtained from the study of genes alone. For
example, proteins, not genes, are
responsible for the phenotypes of cells.
That’s why proteomics came
Types of Proteomics
 Types of Proteomics
• Interaction Proteomics
Most proteins function via protein–protein interactions,
and one goal of interaction proteomics is to identify
binary protein interactions, protein complexes, and
interactomes.

• Expression Proteomics
The quantitative study of protein expression between
samples that differ by some variable is known as
expression proteomics. In this approach, protein
expression of the entire proteome or of subproteomes
between samples can be compared.
A MS workflow for measuring
protein turnover rates in vivo
• Proteins are continually produced and
degraded, to avoid the accumulation of old
or damaged molecules and to maintain the
efficiency of physiological processes.
Despite its importance, protein turnover has
been difficult to measure in vivo. Previous
approaches to evaluating turnover in vivo
have required custom labeling approaches,
involved complex mass spectrometry (MS)
analyses, or used comparative strategies that
do not allow direct quantitative
• Here, a robust protocol has been described
recently on ( 4 November 2019) for
quantitative proteome turnover analysis in
mice that is based on a commercially
available diet for stable isotope labeling of
amino acids in mammals.
• Source:
natureprotocol.com
• Data and code availability
GitHub: https://github.com/malevra/protein-
turnover
Tools of Proteomics
Tools of Proteomics
 Tools of Proteomics
• Protein and peptide separations Done by
• One –Dimensional SDS -PAGE
• Two –Dimensional SDS-PAGE
 Protein Digestion Techniques
• Proteases that are most widely used in proteomic
analysis are
• Trypsin – by far the most widely used protease in
proteomic analysis.
• Glu-C[ v8-protease]
• Other proteases and cleavage reagents
• Lys-C
• chymotrypsin
• Asp-N
• Non specific proteases- subtilysin, pepsin,
proteinase K and pronase
 Post Translational Modification

• Glycosylation-structural components of cell

surface helps in binding
by the receptors and eliciting immune response.
E.g. ABO blood group antigen, Human IgG
•
Phosphorylation – play a role in the regulation
of many cell processes
such as growth and cell cycle control.
•
Sulfation
Techniques of Proteomics
• Proteomes of interest, such as the human
proteome have such complexity that no
single technique is adequate for complete
analysis of the constituents.

• There are so many techniques for

identification and analysis of the proteins in
proteomics such as
Matrix-assisted Laser Ionization etc.
 Two- Dimension Gel
Electrophoresis
• It is a form of electrophoresis which is
commonly used to analyze proteins.
• In this technique proteins are extracted from
chosen specimen .
• Software packages include BioNumerics2D,
Delta2D, Progenesis and PDQuest for
quantification and detection of particular
protein resolved on a gel
 Protomap
• PROTOMAP stands for “Protein Topography and
Migration Analysis
Platform”.

• Protomap a proteomic technique used for

characterizing protolytic
events using mass spectrometry.

• Protomap was invented and developed by Ben

Cravatt and
colleagues at The Scripps Research Institute.
 Protomap -Procedure
• To perform a Protomap analysis proteins are
separated via 1D-SDS-PAGE.
• Protomap is a recently developed proteomic
technique for identifying changes to proteins that
manifest in altered migration by one- dimension
SDS-PAGE.
• It is similar conceptually to two- dimension gel
electrophoresis.
• Protomap is performed by resolving control and
experimental
samples in separates lanes of a 1D-SDS-PAGE gel.
• Each lane is cut into evenly spaced band (usually 15-
30 bands).
• Information from all of these bands are
bioinformatically integrated
into a visual format called a peptograph
• Which plots gel migration in the vertical dimension
(high
to low molecular weight, top to bottom)
• Sequence coverage in the horizontal dimension (N-
t0 Cterminus, left to right)
 Mass Spectrometry
• Introduction

• MS/MS plays important role in protein

identification (fast and sensitive)
• Derivation of peptide sequence an
important task in proteomics
• Derivation without help from a protein database
(“de novo sequencing”), especially important in
identification of unknown protein
3 Major Parts of Mass Spectrometer
• Sours ionized the
sample
• Analyzer separate the
ions on m/z ratio
• Detector sees the
ions and
analyzed the result
 Basic Steps in MS

• Isolate cell or other protein source

• Lyses cells and isolate proteins
• Break up proteins into smaller (but still
relatively large) amino acid chains
• Separate chains (2D gel, gas or liquid
chromatography)
• Analyze separated protein parts by mass
spectrometry
 Mass Spectrum
• Proteins consist of 20 different types of a. a.
with different masses (except for one pair
Leu and Ile)
• Different peptides produce different spectra
• Use the spectrum of a peptide
to determine its sequence
Applications of Proteomics
 Applications
• Most important and promising applications to
come forward is the manufacture and production of
potential new drugs for the treatment of particular
diseases
• Clinical Applications
• Most of the biotech companies now have a
proteomic oriented biotech partner
• Common applications in drug discoveries
include target
• Identification and validation
• Proteins may serve as potential threptic targets
 Clinical Applications
• Drug Discovery
• Functional genomics and proteomics have
provided a huge amount of drug
targets
• Most drugs acts on proteins.
•
For example: Protease Inhibitor is design to
disable protease enzyme that allows particular
virus to reproduce.
•
Majority of drug target are proteins.
• Biomarkers
• A characteristic that is objectively measured and
evaluated as an indicator of normal biological process
pathogenic process , pharmacological response to a
therapeutic intervention is called a biomarker

• In medicine biomarker can be a traceable substance

that is introduced into an organism as a mean to
examine organ function and aspects of health .
• In neurology
• In neurology many applications of proteomics have
involved neurotoxicology and neurometabolism as
well as in determination of several proteomis aspects
of individual brain areas
 References
• Rediscovering biology-protein and proteomics
• Introduction to proteomics-tools for the new biology-
DANIEL C.LIEBLER
• Natureprotocol.com