Tuesday, September 19, 2017

Let's plunder some .PDresult files, matey!

(Wait. There's a guy on our team who dresses as a pirate?!?)

As I'm sure you're aware, it's talk like a pirate day. You can go two ways with a holiday like this as a blogger. You can ignore it completely OR you can make a sad attempt to tie it in with what your blog is about. I, unfortunately, chose the latter.

Recently, I've been helping some people with some impressively complex experiments. The days of "how many proteins can you identify" are just about gone. The days of "how does this glycosylation event change globally in relation to this phosphorylation event and how the fourier are you going to normalize this" Arrr upon us. 

The Proteome Discoverer user interface has gotten remarkably powerful over the years. However, I imagine the developers sit back and have meetings about -- "we have this measurement that is made as a consequence of this node's calculation, but I can't imagine a situation under any circumstances for why someone would want this." To keep from overwhelming us with useless measurements they don't output some of these measurements.

.MSF files and .pdresult files are really formatted SQLite files in (pirate? groan....) disguise. DB Browser uses virtually no space and can pillage these files and reveal all the behind the scenes data. 

For this reporter quan experiment, I can get to:  

78 different tables! Add more nodes into your workflow and there are more! You can get to in and pillage the files for tables you can't access otherwise.

Is this useful to you? Maybe if you're doing something really weird. If the weird thing you are doing is really smart, you could also make a suggestion to the PD development team to include it in the next release.  In the meantime, maybe this will do, ya scurvy dog (ugh...sorry...)

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