Hey -- this, might seem super self-serving, but I don't care. I'm sooooo psyched.
Okay --- so 3 years ago I was staring at the most important dataset that I've ever been involved in generating -- one full of riddles and no perceivable answers and I had an idea of how to maybe look at it in a new way. But the idea had to go on the shelf, because I didn't have the brains, skills, expertise, talent, or brains, or brains to pull off what I wanted to do.
What I needed was a team with all of those things! And this year I found one!! PROOF!
I don't know if anyone else will ever find this tool useful. I know that I'm using it daily (and, if I'm perfectly honest, that's all I care about, but I really really wanted it out there just in case and for everyone to see how smart the people around me are!)
Here is the scenario it was invented for:
I've got 24 fractions of reporter ion quan stuff. The LC-MS/MS was ran by an expert's expert (PNNL, FTW, yo!) and this phenotype is as extreme as you can possibly get. The control channels? Yeah... they were still alive when the samples went on the instrument....
And you know what I have from the total protein quan? Besides some concerns regarding my capabilities as a scientist? NOTHING. And, yeah, today I can delta mass search and I can de novo everything and whatever. There are a lot of tools now that weren't around when I got these files. What if I use these? I get a big ol' list of things. But...if the answer is here in these million spectra? I can't make sense of it. And let's face it, sometimes the best quan software tools aren't found in the same place as the best discovery tools. My favorite tools for discovery don't yet have this kind of quan -- and I need it here.
Okay -- so what if I get RIDAR from Conor's Github here. And I take my MGFs and I say -- only keep the MS/MS spectra that are >2,5, or 10-fold different between my controls and everybody else? (You have to edit the text file, but I've requested a GUI. That's how hard I am to work with, btw.... "Thanks for doing this amazing thing...can you make it so I don't have to open this document, change this number and then save it? That's.too.hard. Thhhaaaannnnkkkkssss.....!")
What does this enable?
1) I know these spectra that RIDAR keeps are quantitatively interesting. Now this opens up tools I love that don't have reporter quan built in. Fragger (is it FragPipe yet?), SearchGUI, Metamorpheus. KER-POW. ALL THE POWER.
2) At 10-fold? I've only got a few thousand spectra -- and you know what they look like? PTM hotspots. Is it real? I don't know yet, but I do know it's the first lead I've ever had on these files. In the study we look at CPTAC data and -- you know what? -- it's similar. Sure, the proteins that change the most come to the top (you'll see bunches of peptides for them, but then you also see loads of spectra that are from one peptide/protein --> and it's PTMs EVERYWHERE.
Sorry if this seems self-promotional (said the blogger, lol!). I didn't make this. It ended up smarter than I ever imagined. (I still don't understand the normalization thing they came up with, but it works!) and now I have a tool I've wanted for years!