PTM discovery with Progenesis SameSpots

I like to discover new things, especially about something already familiar. This week it’s been Progenesis SameSpots and the biochemistry of tear drops. A lot of evidence from our users shows how it helps their research goals with protein differential expression analysis but a recent publication from teams across Australia shows how they applied Progenesis SameSpots to map post-translation modifications and find new proteins in the human tear proteome.

To achieve this required highly-accurate alignment to directly compare three images from the same gel. One was an entire protein map stained with Sypro Ruby, one stained with Pro-Q Diamond to show the phospho-proteins and one stained with Pro-Q Emerald to show the glycoproteins. Progenesis SameSpots made this possible and a great figure (figure 3) in the publication shows a comparison of differentially stained images analysed within the software.

Protein spots showing a positive response to the post-translational modification stains were selected for identification by MS. Other tear protein spots that had not previously been identified by 2D gels were also selected for MS analysis.

There were no significant differences detected in the PTM tear protein profiles, which is a positive in this experiment, unlike the expressional analysis publications we see :). Instead, the important results were:

  • Confirmation of previously identified PTMs in the tears
  • Evidenced for previously undetected protein modifications
  • A novel tear protein, dermicidin, was identified for the first time and this was validated with an MRM-based approach

This publication helps validate some benefits of Progenesis SameSpots, which existing users and anyone new to 2D image analysis may not be aware of. We’ll try to share more examples here as we get evidence to show them.

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  1. […] normally use the blog to highlight interesting applications or benefits people have experienced generating these published results. This month, I updated the […]