S100P levels are linked to recurrence in cholangiocarcinoma

 

It might be easier to make a list of things S100 proteins don't appear involved in at this point.

This paper is going to be posted here because I'm personally interested in it and I wish my lab had access to these samples. 

The samples were analyzed digested with some amount of trypsin. You'll never find out how much, but I bet it is fine. They were also labeled with some kind of TMT reagents. The TMT labeled (and, presumably, pooled) samples were analyzed with a Q Exactive of some kind, probably, despite the Agilent high flow coupled Fusion system in the diagram above. The files are on ProteomeXchange if you cared to look. A secret length and flow rate of a gradient of some length you could extract from the .raw files if you wanted, was used to what was most likely a very reasonable DDA method. They couldn't share the resolution of the MS/MS because that might tip you off to what TMT reagents were used. And if they said they used a 1.4Da isolation window someone would complain about it, as would another group if they used a 0.4 Da isolation window. The authors avoid all that controversy by not sharing any of the steps necessary to repeat this analysis of these same tissues.

That being said - the files are publicly available. It could be one of those things where a core ran the samples and the group never paid them, and the core refused to contribute to the paper. Also, the downstream analysis seems compelling and it looks like they really thought about their stats in this little cohort. We can probably assume that the mass spec stuff was done right. We can also assume that the reviewers and editors had a lot on their plates when this one slid through peer review. And that happens, we're all busy.