Identifying Proteins in a Pierce Intact Protein Standard with ProSightPD 4.0.

This tutorial will guide you through your first search with ProSightPD 4.0 for Proteome Discoverer 2.5. Specifically you will use the ProSightPD 4.0 nodes to search for proteins contained in the Pierce Intact Protein Standard. The tutorial assumes that Proteome Discoverer 2.5, and ProSightPD 4.0 are already installed. If Proteome Discoverer 2.5 or ProSightPD 4.0 is not installed, their installers can be found on the Thermo’s Life Sciences Mass Spectrometry Software Download and Licensing Portal here.

The Pierce Intact Protein Standard is a mixture of six recombinantly expressed proteins to check the health of mass spectrometers prior to running protein samples. This standard mixture will be commercially available soon through Thermo Fisher Scientific.

The Pierce Intact Protein Standard mixture consists of the following proteins:

  • IGF-I LR3 (Peprotech) (9 kDa)
  • Thioredoxin (12 kDa)
  • Protein G (21 kDa)
  • Carbonic Anhydrase II (29 kDa)
  • Protein AG (51 kDa)
  • Exo Klenow (68 kDa)

Follow these steps to perform your first search with ProSightPD 4.0 for Proteome Discoverer 2.5:

1. Ensure that Proteome Discoverer 2.5, and ProSightPD 4.0 are installed.

2. Download the three Pierce Standard medium high raw files.

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3. Download the Medium High Pierce Standard pdAnalysis and the Pierce Intact Standard Proteoform Database.

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4. Follow the steps in this video to install the Proteoform Database for Pierce Intact Standards, and run the search.

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