Software- Diagram of WorkFlow

Instructions:

1. Pre-Requisites- Confirm necessary software is installed & properly configured
2. Mass Spec Set-up Configuration for Data Processing (PKL- PeakList Output)
3. Protein ID (Search Engine)- Mascot Settings & Links
4. Post-Protein ID processing-
   1. Mascot Export- method to create an accessible copy of the Results Mascot's Protein search algorithm generates.
   2. iTRAQ- Extract-iTRAQ-Labels -used to extract and append iTRAQ information to the generic (CSV-format) Results from Mascot Protein Search Algorithm requires perl Programs
5. Collate/Coordinate/Organize Reports-
   • PrepareDataSetReport- package the extended information into a presentable format
   • PeptideCombinationReport- 10 samples are analyzed and Complement C3 is in each.
     • We would like to see a spread sheet showing-
   • Rows- all Peptides used to identify Complement C3
   • Columns- One for each sample anaylzed with the cell showing iTRAQ ratio of peptide in respective sample.
   • ProteinCombinationReport- 10 samples are analyzed with many proteins identified in each sample.
     • We would like to see a spread sheet showing-
   • Rows- all Proteins identified in any Sample
   • Columns- One for each sample anaylzed with the cell showing iTRAQ ratio of protein in respective sample.
6. Excel Tips- Helpful suggestions when working in Excel- covers Printing, Freezing, and Protecting.