Mass Spectrometry Workstation Layout

1

Building Research Infrastructure
Jay L. Hess M.D.
Ph.D. University of Michigan Department of
Pathology
Arul Chinnaiyan Lab website
2
Research Infrastructure Planning Process

• Departmental research goals
• What are the needs?
• What options are available to meet
  need?
• 1. Structure
• 2. People
• 3. Space
• 4. Hardware
• 5.

3
Departmental Research Goals be a
national leader in - Molecular oncology
(esp. epigenetics) - Pathology
informatics - Development of innovative
technologies in diagnostic pathology
4
What are the research needs?
Autoantibody signatures in prostate cancer Wang
et al. NEJM 3531225, 2005 Tissue
banking Robotic arrayers Imaging Informatics Mass
spectroscopy Flow cytometry Mol path services
5

• What options available to meet need?
• Do nothing (let the PI take care of it)
• - Inefficient
• - May be impossible to get the work done
• 2. Existing core facilities
• - Great when they work well (routine
  services),
• but often they dont
• - If good but overworked, consider
  partnering
• Create a new core facility
• - Institution-wide
• - Do you really want to be in this business?
• Create departmental resource facility
• - Best for highly specialized,
  technology-intense
• research

6
Research Infrastructure Structure
Creation of two new research divisions
7
Division of Translational Research People
Kojo Elenitoba-Johnson M.D.
Molecular Pathology
Flow Cytometry
Tom Giordano M.D. 3 FTE
Lloyd Stoolman M.D. 0.5 FTE

• Analytic flow
• cytometry

• Tissue banking
• Laser capture microarray
• Tissue microarray
• Tissue imaging
• Quantitative antigen
• detection (AQUA)
• Mol pathology lab

• Protein identification
• Post-translational
• modifications
• Complex mixtures
• ICAT
• MudPIT

Center for Molecular Pathology

• Arul Chinnaiyan M.D. Ph.D.
• High throughput FISH
• Array CGH
• Protein array
• Microarray
• Bioinformatics

8
Division of Translational Research Hardware
Thermo Electron LTQ Mass Spectrometer

9
Division of Translational Research Hardware
G SIM microarray spotter

10
Division of Translational Research Hardware
Meta Systems robotic imaging station

11
Division of Translational Research Space
Mass Spectroscopy Laboratory
1600 sq feet plus 2 offices
12
Division of Pathology Informatics People
Clinical Informatics Research
Informatics
Ul Balis M.D. Arul
Chinnaiyan M.D. Ph.D.
Bruce Friedman M.D. 16 FTE- Path Data Systems
1 FTE- computer cluster support 1 fellow
Alexey Neshvizhskii Ph.D. Dan Rhodes Ph.D. Lloyd
Stoolman M.D. Jules Berman M.D. (adjunct) 1 FTE -
programmer 1 FTE - MS data analysis 0.5 FTE-
slide imaging

• LIS
• Computer hardware including high- performance
  computer cluster
• Custom interfaces
• Web Page
• Slide scanning
• Image analysis
• Resident teaching
• Informatics fellowship

• Oncomine
• MS data analysis
• Bioinformatic support
• Sponsored research

13
Division of Pathology Informatics
14
Division of Pathology Informatics
Informatic Support for Mass Spectroscopy Facility
15
Division of Pathology Informatics
Scott Tomlins Arul Chinnaiyan
www.oncomine.org
16
Meta analysis of microarray data- one example
Cancer Outlier Profile Analysis (COPA)
What does oncomine do
Scott Tomlins Arul Chinnaiyan
17
Division of Pathology Informatics - current
projects
18
Division of Pathology Informatics - current
projectsHistoMine

19
HistoMine
Division of Pathology Informatics - current
projects
20
Division of Pathology Informatics Hardware
Computer room

21
Division of Pathology Informatics Hardware
Aperio Slide Scanner

22
Division of Pathology Informatics Space

2400 sq feet plus 750 sq ft computer room
23
Long-term infrastructure plan Pathology
Institute Centralize clinical, educational
activities and molecular oncology, informatics
and translational pathology programs into a new
building (90,000 net sq ft clinical, 30,000 sq
ft res)
24

• Question for Discussion
  
• How should these Departmental Resources be
  funded?
• 1. No fees - Eternal Department subsidy
• 2. No fees - Hope the growth in indirect costs
  pays for
• them
• 3. No fees - Fund them as cores on programmatic
  grants
• 4. Fee for service- If so, what is a reasonable
  cost recovery?