Overview

PiMS can group a number of Targets together as a Complex.

Contents

• Create a new Complex
• The View of a Complex
• Co-expressing a dimer
• Assembly of a construct from separately expressed protein
• Report the progress on a complex to SPINE2 Target Tracker

Guide to using PIMS.

Complex management

• Create a new Complex

  To record a Complex in PiMS:
    select Create a New Complex from the Target and Complex menu
  
  
  
  

  • All fields are mandatory -as indicated by the red * after the field names
    
    
  • Give your complex a name, and indicate why it was chosen.
    
    
  • Then add any other information you wish.
    
    
  • When you have completed all of the mandatory fields click the button
    The Complex will be recorded and displayed in a PiMS Complex details view.
    
    

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• Complex Details

  You can see the details of your complex in the view complex page. Here you can also add new components, or remove components from your structure.
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• Co-expressing a dimer

  PiMS provides standard protocols for co-expressing a dimer.

  If both PCR product nucleotides are cloned into the same plasmid the PiMS Bicistronic Infusion protocol can be used.

  When a different plasmid for each protein is in the transformed cells, the PiMS Bitrans Transformation protocol should be used.

  Of course you will probably want to tailor these protocols to match your particular experiments.

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• Assembly of a construct from separately expressed protein

  Similarly a complex assembled from separately expressed proteins can be represented in PiMS.

  A protocol such as the standard PiMS Co Concentration should be used. This allows two separately purified proteins to be added for the concentration stage.

  You should make you own protocol to allow more than one protein sample to be input at the scale up step appropriate for your experiments.

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• Report the progress on a complex to SPINE2 Target Tracker

  The SPINE2 target tracker is a central repository that allows the progress of SPINE2-COMPLEXES to be reported and publicised. PiMS can report to the target tracker on the status of targets and complexes it is recording.

  PiMS data is exported into an XML file which can then be imported into the SPINE2 target tracker. To export the PiMS data, find the view of the final PiMS sample, this would normally be concentrated protein. In the view of samples produced from experiments, there is a link to the Target to Crystal report.

  

  The Target to Crystal report is a summary of the history of a sample. It can also be printed as a pdf (select Export to PDF).

  If the sample can be linked back to a complex, there will be a button labelled Export to Spine2. Select the Export to Spine2 button to generate the xml needed for the target tracker import.

  

  The xml should be saved (File - Save Page As) to a folder on your network. In the Spine2 target tracker TargetTracker Home page, there is a link in the Tasks list to Import data. Selecting this link will open the Upload external data page and allow you to browse to find your import data.

  

  The spine2 target tracker checks that external meets certain criteria before it can be uploaded. A complex must contain targets and constructs, and experiments and samples must all reference these objects. In the workflow below, both complexes contain both of the targets, and all of the experiments can be traced back to constructs of these targets. This workflow can be uploaded.

  

  The next workflow shows that one of the PCR products in the Bicistronic Infusion experiment can be traced back to a target which is in complex B, whilst the other from a target which is not in this complex. In this instance the workflow is unsuitable for spine2. A new complex would need to be created that contains both of the targets.

  
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