PerkinElmer Life Sciences Production Company Meeting - 1st February 2002 Progenesis

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PerkinElmer Life Sciences Production Company
Meeting - 1st February 2002Progenesis
John Hoyland Product Manager - Bioinformatics
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What is Proteomics?

• The total PROTEin complement of a genOME.
• M. Wilkins et al. Electrophoresis 1995, 16,
  1090-1094
• Proteome describes the complete set of proteins
  that is expressed, and modified following
  expression, by the entire Genome in the lifetime
  of a cell.
• In essence, it describes the complement of
  proteins expressed by a cell at any one time.
• Proteomes are highly dynamic
• Proteomics is the study of protein properties on
  a large scale to obtain a global, integrated view
  of disease processes, cellular processes and
  networks at the protein level.

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Why are Proteins important?

• Proteins are actively involved in a large number
  of disease and genetic medical conditions
• Proteins are a primary target for new drugs to
  combat these conditions
• If we can identify the proteins which are either
  missing, or are present when they should not be,
  we have a good chance of developing a drug to
  correct it.
• In order to identify individual proteins, we must
  first separate them to analyse them independently

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How do we separate Proteins?

• 2D Gel Electrophoresis
• Different Proteins have different sizes or
  molecular weights
• Different Proteins have different charges or pH

• However
• Some Proteins have the same size or molecular
  weight
• Some Proteins have the same charge or pH

• We therefore need to separate them for both size
  and charge
• Separate in the X dimension for charge
• Separate in the Y dimension for size

• This gives us a 2 dimension (2D) map of the
  protein spots which can be imaged and analysed

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2D Gel separation of Proteins

• To see the proteins we must stain them

• ProXPRESS images both fluorescent and
  non-fluorescent stains

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Comparing images of gels

• Now we have separated them, we may need to
  compare the images of large numbers of gels to
  see which proteins are present and which are
  missing
• Looking for the differences in 50 or 100 gels
  with between two and four thousand protein spots
  on each is not unusual
• Making these comparisons is also NOT EASY and
  very time consuming. It is the major bottleneck
  in Proteomics

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Where is the bottleneck?
2D Gel Electrophoresis
Staining
Image capture
Feature Excision
Protein Digestion
Image Analysis
Image Analysis
Identification
Identification
MS Preparation
MS Analysis
Database
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What was needed?

• A 2D gel analysis system
• Automatic
• Reproducible
• High throughput

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Progenesis - automatic

• Progenesis is a hands-free, walk-away automated
  2D gel analysis package for medium to high
  throughput proteomics.

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Smashing the bottleneck

• Assume we have 50 protein samples to compare

• Using HT Analyser, elapsed time and hands on time
  are similar so this is a full time job for a
  skilled user - maximum throughput 50 gels per
  MONTH

• Using Progenesis, elapsed time is only 1 week
  with only 3 days skilled user time -
• - maximum throughput 100gels per WEEK

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The Analysis Wizard
Select Gels to Analyse
Group them
Define Reference Gel
Define Background Subtraction
Add Filters
Define Normalisation
Add Warping and Matching
Save this Protocol
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Automated spot detection

• Automation the key to high throughput
• Every spot is detected accurately and objectively
• Walk away with confidence that each image is
  treated using the same processes

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Objective

• Automatic objective spot splitting

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More targets than ever before

• Progenesis delivers
• More true spots, more targets
• Objective and operator independent
• Increase in detected expression from 2D gels

Traditional - auto 465 spots
Progenesis 686 spots
with edit 432 spots
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Progenesis Analysis Summary

• Automated Analysis
• Robust detection of every spot
• Warping enhances matching

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Identification of interesting proteins

• Proteins that look like they have been up
  regulated or down regulated can be selected for
  further analysis
• Spots are cut out of the gel by ProPic, our
  automated spot cutting robot

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Export Picking List to ProPic

• Use Progenesis to find and select spots for
  picking
• Built in Export to ProPic option generates
  picking list

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Final Identification

• After processing to separate the proteins from
  the gel, they are analysed in a Mass Spectrometer
• The Mass Spectrometer separates and quantifies
  all elements in the protein
• Each protein has a unique fingerprint of
  constituents which may be checked against massive
  databases to identify it

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Target Accounts

• Target accounts Pharmaceutical Companies with
  Proteomic research facilities
• University and academic core proteomics
  facilities
• Any Proteomic group analysing more than 10-15
  gels per week
• We have four specialists supporting Progenesis
  sales one in Europe, two in USA/Can and one
  Asia/Pacific

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Is it value for money?

• Many researchers think so
• In the first 6 months we have over 70 leads
  worldwide
• Sold 3 copies in first 6 months

• Pharmaceutical Companies
• It now costs around 800M to get a major new drug
  on the market
• If Progenesis reduces this by a fraction of 1 it
  saves its cost

• Compare Progenesis automation with old manual
  methods
• If a Proteomic facility is running 100 gels per
  week
• Progenesis pays for itself in just 10 weeks

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Finally-

• At the start I mentioned 2 bottlenecks
• The second revolves around managing the huge
  amounts of data generated by Proteomics
• The next project will be Progenera, a databasing
  and data mining package from Nonlinear Dynamics
• Progenera will be on the market by September 2002

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Delivering the future of Bioinformatics