TDCollider 1.0 Demo 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 & ProSightPD Demo Data

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

ProSightPC 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:

 

Identifying Proteins in a Top Down Standard with ProSightPD 1.1.

A simple mixture of five proteins is used by the National Resource for Translational and Developmental Proteomics to check the health of their mass spectrometers prior to running clinical samples.

The Top Down Standards mixture consists of the following proteins:

  • 1 pmol myoglobin (M5696)
  • 0.5 pmol trypsinogen (T1143)
  • 0.5 pmol carbonic anhydrase (C2624)
  • 0.1 pmol ubiquitin (U6253)
  • Superoxide dismutase – SOD1 – contaminant is present in carbonic anhydrase

An example RAW file containing data of Top Down Standard proteins can be downloaded and searched against a custom ProSightPC database to identify proteins in the standard’s mix.

A search can also be performed in ProSightPD as a quick exercise to check that ProSightPD is working correctly on your computer prior to attempting analyses of your own files.

Following these steps to do this analysis:

1: Ensure that both ProSightPC 4.1 and Proteome Discoverer 2.1 are installed on the computer on which you intend to run this exercise.

2: Download both the ProSightPD 1.1 Installer and the Quick Start Guide.

3. Follow the steps in the Quick Start Guide to install ProSightPD 1.1.

4. Download the Standards .raw file, the Proteoform Database for Top Down Standards, and the corresponding flat file.

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5. Follow the steps in this video to install the Proteoform Database for Top Down Standards, and run the search.

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/