How do I create a Progenesis SpotCheck gold standard?

To get started with Progenesis SpotCheck you need a gold standard. Progenesis SpotCheck will use your gold standard as a baseline to objectively measure the quality of your gels.

A gold standard is made from gels that have been run using the same sample and following the same protocol. It should only contain gels that you are happy with and are representative of the quality you aim to maintain in your lab. As well as considering how well the gels have run and how well the protein spots have been resolved, you should also make sure the images have been captured satisfactorily. The Image QC stage at the start of the Progenesis SameSpots workflow is a useful way to check the image capture. There is also some advice on gel running protocols and image capture available here.

Once you have the images for your gold standard, open Progenesis SameSpots, create a new experiment and add your images. Make sure the images have passed all of the image quality checks and make sure the images are all in the correct orientation. They can be cropped, flipped and rotated if necessary.

Next, press the Section Complete button to continue through the Progenesis SameSpots workflow. As with any Progenesis SameSpots experiment, alignment is a crucial step. You should expect a gold standard set of images to align fairly well automatically, but it also worth spending some time reviewing the alignment and correcting any misalignments as necessary.

Next, you should use the Filtering step to remove any small, noisy spots, etc. This it to make sure that SpotCheck can measure the quality of the real protein spots in your gels without any false spots clouding the results.

This is as far as you need to go in the analysis to create a gold standard. Select Close from the File menu to save the experiment and take you back to the start page of Progenesis SameSpots.

Switch to the SpotCheck quality control tab and press the Convert an experiment... button. Here you will select the experiment to use as the gold standard and set the criteria you want any test gels to meet.