wiki:WorkingWithSamples

Samples and sample tracking

Proteios provides possibilities to annotate and track samples through the proteomics workflow. In the Proteios (and Base) vocabulary, samples are the unprocessed biomaterials. Usually these are subjected to some kind of protein extraction, and the result is an extract. Extracts are used for separations like isoelectric focusing, gel electrophoresis or liquid chromatography. They can also be labeled with a fluorescent dye, to generate a labeled extract.

Samples can be annotated with information, and also with files.

Events

There are several activities that use biomaterials, and these are recorded as events in Proteios. Events hold information about execution times and the protocols that have been used. A creation event is the event that created a biomaterial, for example the process of protein extraction or labeling of an extract with a CyDye.

A separation event is liquid chromatography, isoelectric focusing or gel electrophoresis. Some of these events are associated with an object, for example an IPG strip or gel, which in turn have an external identifier and information like pH interval or gel size.

Gels can be subjected to staining events and gel scan events. The later events can be associated with a raw image file.

Protocols

Protocols are used to describe common tasks in the lab. A protocol can be connected to a file, for example a text document describing how a 1D gel is run. To create a protocol, first upload the file. Then check the select box next to the file and click 'Extensions'->'Use as protocol'. Currently only users with the 'User' role can create protocols.

Batch import

Sample data can either be input via the GUI or via batch import, in which case the data is contained in tab-delimited format in an input text file. To create samples using batch import, first upload the input file. Then check the select box next to the file and click 'Extensions'->'Batch import from tab-delimited input data'. The contents of the input files will be checked and a page displayed with information on the parsed data. If the parsing is correct, click tool-bar button 'Create import job[s]' to create an import job. For more information on batch import and the format of the input file, see Batch Import Of BioMaterial Items.

Examples

Adding a 2D gel

There are several ways to add a 2D gel. The easiest is probably to start from an extract:

  1. From the extract view, select 'New Separation Event' and then 'IPG' in the next step. You will then be asked to add information about the IPG strip, including the external ID which could be the bar code of the strip. In the next step the information about the actual event is added, that is protocol and how much extract was used etcetera.
  2. You will then be back at the extract screen, and then information about the second dimension is added by selecting 'New Separation Event' followed by 'GelElectrophoresis'. For the gel you can choose a gel which have been added previously without sample information, or to generate a new one. After selecting an existing gel or creating a new one, you have to enter information about the actual event. For used quantity you should set 0, since no extra extract was used for this dimension. You will be transferred back to the extract view afterwards.
  3. The two dimensions will be listed at the bottom of the page. Only thing that remains is now to link the two dimensions: Select 'Gels' in the left frame and click on the gel which you just created. In the 'Previous Dimensions' table there will not be any information about the IPG. Select 'Add Previous Dimension' and select the IPG separation. Back in the gel view again you will find the IPG separation listed.
  4. To add information about staining, select 'New Staining Event'.
  5. To add information about scanning and to attach a image file, select 'New Gel Scanning Event'.

Adding a DiGE gel

To add a DiGE gel you need to start with at least two labeled extracts, with different dyes.

  1. Label extracts by selecting 'Label Extract' in the extract view.
  2. From the extract list view, select 'Add DiGE'.
  3. Specify how much (microliter) was used of the different labeled extracts.
  4. Add information about the gel.
  5. Add information about the IPG.
Last modified 12 years ago Last modified on Sep 30, 2009, 2:55:08 PM