Okay -- y'all know that depressing conversation, right?
You've prepped a ton of samples
You've phospho-enriched and fractionated and your QA samples are great and your internal QC standards are perfect.
You've crunched the data painstakingly to generate this amazingly well-curated list of proteins and their quan and the relative quan of thousands of phosphosites --- and you're presenting it to the people that procured these priceless samples and you hand over the results.
And...they...quietly...stare...at...you.....
"Wait," they finally say, "Is that it?"
"You're not done, are you?"
"What am I going to do with a list of thousands of differential phosphosites?"
And you think, or if you're me, you actually say,
"No idea! Best of luck!" Remind them that they agreed to the hard stop so you could run to your next meeting!
Cause -- fuck if I know what to do next. Its been almost 10 years since I did my first SILAC phosphoproteomic study -- that OrbiXL only came back with a few hundred confident phosphopeptides. And a few dozen changed. So I looked 'em all up and it kindof made a story. You can't do it that way (well...I can't...I'm getting hella old) with 3,000 sites you got off of today's instruments....
WHAT IF THIS IS FINALLY THE THING THAT CAN MAKE SENSE OF PHOSPHO PATTERNS?!!??!
Check out this GitHub thing. It's full of amazing tools!!
Check out the MCP paper that describes them!
Then write me and tell me if this is finally THE THING WE'VE BEEN WAITING FOR! (Please) You know what I'm talking about. I'm not getting my hopes up. I've fell for it before. But -- for real -- maybe this is it!
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