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1. Peptide hits validation
Validate the peptide hits returned by the mass-spectrometry peptide identification algorithms
- Deliverables:
- reports generated by peptideProphet
- Tools Used:
- peptideProphet: (Nesvhizskii et. al. http://peptideprophet.sourceforge.net) used to validate peptide hits:
- pepXML output file that has list of validated peptide hits.
- pepXML output file that has list of validated peptide hits.
- peptideProphet: (Nesvhizskii et. al. http://peptideprophet.sourceforge.net) used to validate peptide hits:
2. Protein hits validation
Validate the protein hits using the pepXML peptideProphet output
- Deliverables:
- reports generated by iProphetProteinProphet
- Tools Used:
- iProphetProteinProphet: (Nesvhizskii et. al. http://proteinprophet.sourceforge.net) used to identify high-confident protein hits
- protXML output file that has list of validated protein hits.
- protXML output file that has list of validated protein hits.
- iProphetProteinProphet: (Nesvhizskii et. al. http://proteinprophet.sourceforge.net) used to identify high-confident 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: (Marcotte et. al.) http://www.marcottelab.org/APEX_Protocol/)
- List of differentially expressed proteins
- List of differentially expressed proteins
- APEX: (Marcotte et. al.) http://www.marcottelab.org/APEX_Protocol/)
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.
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