Proteomics indicates a strikingly strong pathway in an Alzheimer's mouse model

I'm going to admit right off the bat that I didn't read this whole paper. Mouse neuro- stuff is something that I'm not entirely comfortable thinking about, so if you mention in your methods you did "contextual fear conditioning as described previously" I'm not following that link for the details.

 What I do know? This study used a mouse Alzheimer's model and found a differentially regulated pathway that lit up like an airport runway in the midwest.

I'm going to start by assuming their model makes sense so I don't have to read any of those parts. In general, though, they took brains from their normalish super inbred mice and brains from their disease model inbred mice and extracted the hippocampal region. Having some experience in this sample prep technique, its worth noting that once you get past the vivid daylight hallucinations of the mice politely requesting their brains back, you're over the hump. The nightmares are relatively infrequent over the following 6 years or so.

The hippocampal regions were FASP digested, and separated on a 10cm nanoLC column over a 5 hour gradient on their Orbitrap Velos as they previously described in a study a few years ago. I find it somewhat remarkable that a 10cm column could contain enough theoretical plates to adequately make use of a gradient this long, but they again report a striking number of identified peptides/proteins. (~2,600 found in 3/4 samples).

Relative quantification was performed using spectral counting and normalization in: Visualization and downstream analysis in IPA.

What did they find? 103 statistically significantly disregulated proteins that all seem to fall right into a canonical pathway. When I mention proteomics in terms of neuro samples, I'm often met with the suggestions that this stuff is incredibly difficult. And I'm not trying to downplay the capabilities of this group. They are clearly experts in this technique, but around the sample prep this is a pretty straight-forward method that leads to as clear of a set of conclusions as I've seen.