TDCollider 1.0 Demonstration Data

The following data file is available for use with TDCollider 1.0:

golden_2016_06_02.tdReport

 

Identifying Proteins in a Pierce Intact Protein Standard with ProSightPD 1.1.

This tutorial will guide you through your first search with ProSightPD 1.1 for Proteome Discoverer 2.1 and ProSightPC 4.0. Specifically you will use the ProSightPD 1.1 nodes to search for proteins contained in the Pierce Intact Protein Standard. The tutorial assumes that Proteome Discoverer 2.1, ProSightPC 4.0, ProSightPD 1.1 and ProSightPD 1.1 with High Mass are already installed. If Proteome Discoverer 2.1 is not installed please contact your local Thermo Sales representative. If ProSightPC 4.0 is not installed, you can find the installer and installation instructions here. If ProSightPD 1.1 is not installed, you can find the installer and installation instructions 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 1.1 for Proteome Discoverer 2.1 and ProSightPC 4.0:

1. Ensure that Proteome Discoverer 2.1, ProSightPC 4.0, ProSightPD 1.1 and ProSightPD 1.1 with High Mass 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.

 

ProSightPC 4.0 Demonstration Data

The following data files are available for use with ProSightPC 4.0 and ProSightPD 1.1. Example analyses can be found in the User’s Guide and Quick Start manual.

ProSightPC 4.0 Demo Data.zip

Human_nuclear_extract_Top_Down_LTQ_FT_MS_MS.raw

PheATE_126kDa_Trypsin_Hi_Hi_Top3.raw

Ubiq_CID_857_50sc_100K_1_8559.616.raw

Ubiq_CID_857_50sc_100K_1_XT_00001_M_8559.616.raw

Online Slide Decks

Several slide decks related to top down proteomics are available for free download. These include:

An overview of top down proteomics:

 

A short overview of ProSightPD:

 

An introduction to the ProSight World of Tools:

 

Learn more about purchasing ProSightPC

ProSightPC

Learn more about purchasing ProSightPC from Thermo Scientific here.

Use the ProSight Lite App

ProSightLite

Use the free ProSight Lite application available from Northwestern University for characterizing a single protein sequence. Download the software from here: http://prosightlite.northwestern.edu/.

Learn More About Top Down Proteomics

Consortium-for-Top-Down-Proteomics

Learn more about Top Down Proteomics from the Consortium for Top Down Proteomics website: http://www.topdownproteomics.org/