Proteomics Technologies

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Proteomics Technologies
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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
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Proteomic Technologies

• 2D gels
• Liquid chromatography
• Peptide digest first
• MALDI or LC/MS, MS/MS
• SELDI
• Microarrays, labeled proteins

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Proteomics Standardization Issues

• Instrument output format
• Data archiving
• Data exchange format
• Data validation
• Data mining
• Data reporting standards

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Instrument output format

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

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Data Archiving

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

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Data

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

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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

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Data Mining

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

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Data Reporting Standards

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

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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