Tuesday, October 7, 2008

Heuristically Beneficial Artifacts

I've recently embarked on a study to see what effect clustering mass spectra has on the design of MRM experiments. Specifically one clusters spectra from the shotgun proteomics discovery phase of the experiment to see how it affects the selection of peptide species and the transitions that a mass spec looks for during the second targeted sequencing phase of the experiment.

While the work is ongoing, a very interesting (at least to me) result has come out of plotting the unfiltered SEQUEST results from the non-clustered and clustered version of the mass spec data. The say a picture is worth a thousand words, so:

The chart is showing the XCORR values of the clustered spectra plotted against the XCORR values for their respective members, independent of what peptide was identified for each. The color coding represent scores for peptides that are part of the decoy database, where:

  • blue = a decoy hit was scored in the clustered spectra, but not the original
  • green = a decoy hit was scored in the original spectra, but not the clustered spectra
  • red = both spectra scored a decoy peptide
What you'll note is that spectra that all clustered score a different set of peptides higher than do the original spectra, and vice versa. At least for this data set, which is SILAC labeled, we note that each method is identifying a different population of peptides. This goes against all current publications, so I have to be careful in the interpretation of these results and will need a significant amount of validation experiments, but this is exciting stuff!

Particularly, it is going to be very interesting to see whether clustering actually helps or hinders ion selection when designing MRM experiments. If it does help ion selection, I have already come up with the catchy name, Heuristically Beneficial Artifacts TM. If not, well, we will at least have looked at the real-world effects of a methodology when applied to a new type of experimental goal.
More on this as it develops.

Monday, October 6, 2008

Not so much about science...

So in looking back over that last few entries, it seems I have strayed from my original mission, which was to cover issues regarding informatics and how it relates to science. The first part seems to have dominated the posts recently, so I am dropping all pretenses starting a new blog, over at Blogger competitor Wordpress.

Why a new platform? I figured I would give Wordpress a spin to see how it compares to blogger. Also I like the template they had for the blog ;) So far, the interface is similar, but looks a bit cleaner than Blogger's. Overall, it seems the same functionality and workflow, with the addition of one thing that I can see coming in very useful for a site like I envision, permanent pages.

In effect, If I write something that I want to be prominently displayed at all times, I create a page. This can come in handy say, if I give a set of instructions for setting up your development environment, or for providing a listing of resources. As a regular blog post these types of items are "discoverable" by searching, but they will eventually go away as new posts drown them out.

Another agument for the Page as opposed to a post is to combat a post from becoming stale. How many times have you thought you found an answer to a question in a blog post but it turns out said post is a bit old and the solution no longer applies? I guess stackoverflow seeks to remedy this, but bloggers can do their part by posting "important" and generally applicable posts with prominence as a page, thus they are always reminded to update it, since is it always visible.

Anywho, there I go again, talking strictly about web applications. Well, I guess I'll shut up now and you can check AppMecha for more posts related to these issues.