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Title:

Proteomics Technologies

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Biospecimen Collection. Mouse Models. Proteomic Technologies. 2D gels ... Mass Spec. Peptide/Protein Sample Preparation. Biospecimen Collection. Mouse Models ... – PowerPoint PPT presentation

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Title: Proteomics Technologies


1
Proteomics Technologies
2
Proteomics Technologies to Facilitate Biomarker
Discovery
Sites of Proteomics Technology Development
Mouse Models
Biospecimen Collection
Peptide/Protein Sample Preparation
Lab 1 Affinity Methods
Lab 2 Mass Spec
Lab 3 Mass Spec
Cross Validation
Cross Validation
3
Proteomic Technologies
  • 2D gels
  • Liquid chromatography
  • Peptide digest first
  • MALDI or LC/MS, MS/MS
  • SELDI
  • Microarrays, labeled proteins

4
Proteomics Standardization Issues
  • Instrument output format
  • Data archiving
  • Data exchange format
  • Data validation
  • Data mining
  • Data reporting standards

5
Instrument output format
  • PE Biosystems (.PKM)
  • Bruker
  • Finnigan (.ASC)
  • Micromass (.PKL)
  • Ciphergen Biosystems
  • Protogen
  • Thermo LabSystems

6
Data Archiving
  • Data base schemas
  • Spectrum information
  • Ontology
  • Common Data Elements
  • Vocabulary

7
Data
  • Emerging standards
  • mzXML
  • mzData
  • PSI-MS
  • MIAME
  • MIAPE
  • caBig
  • Other data sources
  • HUPO
  • NCBI
  • Protein DB

8
Data Validation
  • Noise to peak
  • Specificity
  • False positives, as much as 50
  • Automatic validation using statistical algorithms
  • Manual validation
  • Gold reference standards needed
  • Quality control and quality assurance standards
    for data repositories

9
Data Mining
  • Which algorithms are more effective?
  • Support Vector Machines
  • Random Forrest
  • Neural Networks
  • Decision Trees
  • Fussy Logic

10
Data Reporting Standards
  • Need data reporting standardization
  • Quality control and quality assurance standards
  • Data curation

11
Proteomics Technologies to Facilitate Biomarker
Discovery
Sites of Proteomics Technology Development
Mouse Models
Biospecimen Collection
Peptide/Protein Sample Preparation
Resource Pipeline
Data Pipeline
Lab 1 Affinity Methods
Lab 2 Mass Spec
Lab 3 Mass Spec
Cross Validation
Cross Validation
CaBIG
Common Resources
  • Data Management
  • Common Data Elements
  • Data Standardization
  • Ontology
  • Vocabulary
  • Peptide Synthesis
  • Antibody Solution
  • Antibody Characterization
  • Repositories
  • Distribution

Research Community
Specimens
Data
Antibodies
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