Protein Profiling


The MSB-05, 06, 07, and 08 services are designed to enable protein profiling of samples of vary complexity. The services differ in the total amount of instrument time dedicated to an analysis. The amount of instrument time for each service is 1, 5, 10 and 20hrs for MSB-05, 06, 07 and 08, respectively. Broadly speaking the greater the amount of instrument time, the greater the number of proteins identified and higher the sequence coverage of those proteins. To help you understand the relationship between instrument time and sensitivity we have provided service note with a simple ruler using a whole cell lysate as a case study.

Steps Involved

  • Sample preparation: SDS-PAGE with multiple band excision and in-gel digestion.
  • LC-MS/MS: Increments of 0.5hr LC-MS/MS
  • Data analysis: Protein identification is performed with Mascot. Protein visualization and validation is performed with Scaffold.
  • Report generation: PDF/Excel/Scaffold

The turnaround time is 2-3 weeks.


  • Written Report containing details of your samples, our methods and a summary of the data.
  • An Excel workbook containing the detailed qualitative and quantitative protein identification data.
  • A Scaffold file to enable your own deeper data mining.

An example report is available upon request.

A service note with some data outlining some fundamentals of the service is available here.