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Differential Protein Expression Analyses

Differential protein expression analyses, 6 hour minimum ($282 internal, $360 external) per project.

1. Peptide hits validation

Validate the peptide hits returned by the mass-spectrometry peptide identification algorithms

Deliverables:
- reports generated by peptideProphet

Tools Used:
- peptideProphet: (http://peptideprophet.sourceforge.net) used to validate peptide hits:
  - pepXML output file that has list of validated peptide hits.

2. Protein hits validation

Validate the protein hits using the pepXML peptideProphet output

Deliverables:
- reports generated by ProteinProphet

Tools Used:
- ProteinProphet: (http://proteinprophet.sourceforge.net) used to identify high-confident protein hits
  - protXML output file that has list of validated protein hits.

3. Differential protein expression analyses

Identify differentially expressed proteins as well as absolute protein counts

Deliverables:
- Excel file that has list of differentially expressed proteins (for more than 1 sample) or just absolute protein counts (for a single sample)

Tools Used:
- APEX: (http://www.marcottelab.org/APEX_Protocol/)
  - List of differentially expressed proteins

Note: This analysis needs peptide/protein hit lists from mass-spectrometry search algorithm run on raw-data. If this is not available, we can do this for you. Please see Protein Identification and Validation.