My favorite proteomics stuff of 2014

I was reading an opinion piece I found on Reddit this morning that said there were far too many "Best of 2014" articles out there.  Which reminded me that I hadn't written mine yet!

In case you care, here are my favorite Proteomics News stories of the year!!!  Man, there is soooo much...this may need to just be a small portion.

I'm going to call 2014 the year of quality control in proteomics!  The Pierce HeLa digest was released and so many people are using the PRTC standard or similar things to keep accurate metrics on their samples.  We also saw new QC programs such as qcML,  QuaMeter and nodes for Skyline.

2014 also saw the release of my all time favorite free de novo sequencing software the DeNovoGUI.  This has been an incredible year for software in general:  ptmRS?   Byonic in PD?   MS-Viewer? Peptide Shaker?  Proteo Suite?  Just a ton of cool stuff.

This is the year we really started to see people leverage the power of comparing RNASeq variant data to shotgun proteomics data.  (Another paper: proteogenomics of cancer!) It still isn't trivial, by any means, but some great new tools are on the way (particularly some streamlined stuff out of Minnesota..more on this awesome stuff later!)

Of course, the big news was this stuff:

Sure, it may be a bit controversial, but after ruminating on this for 7 months or so, this is my opinion:  this was a really good thing for us.  The genomics people have been able to say for years "we can see every gene."  Think about where "proteomics" was when the term was coined.  We could load up gel slices on an LCQ and if we came back with 300 proteins that was a big freaking paper. People outside our field who jumped on the proteomics bandwagon 10 or 15 years ago and were turned off may not have ever stopped to see the light years we have come in that time. This cover says in bold terms: we're here and if you give us the resources we can beat the genome sequencers. Hands down.

Instrumentation, wise, this was another great year:  QE HF?!?!  The mass spec we all knew was coming, but is more awesome than any of us guessed?!?  w00h000!  The small molecule crowd also ended up with their own version of the Q Exactive (the focus!) but that awesomely cheap box isn't something that we'll be using.  Kind of on the instrument side of things, someone finally started building computers for Proteomics Data Processing.  I know I probably go on about this too much, but once you've searched a whole cell digest file in 2 minutes for the first time you feel pretty dumb for ever waiting days...or weeks...for a bunch of fractions to finish up!

To wrap this up, I'm gonna revisit my favorite papers of 2014.

XMan: A cancer database with every currently known cancer mutation.  Yes, I'm biased, as it came out of my mentor's lab. It's one of those papers, though, where you're thinking "why didn't I come up with this?"

Labeled and unlabeled intact protein quantification.  Come on, we all want to get there. Top down is the future, its just too freaking hard still, but here we see the use of available tools that remove one of the limitations.  Top down can be quantitative!

The MSAmanda paper came out in June!  We need to get off this addiction we have to these search engines from the 90s.  Yes, they're good. But new algorithms are going to be necessary to really dig into all of this data we're generating.

My early pick for my favorite paper of the year still makes this list:  The Proteomics Ruler!

Its really tough, there is so much good stuff out there this year. I try really really hard but I know I didn't read 10% of what is out there. I probably didn't read 10% of this year's abstracts.  The paper I'm going to refer to the most in 2015 is probably this one from Max Planck.  Systematically step by step how to fully optimize a QE and a QE HF?  I have a day job and I'll be carrying a copy of this paper to work with me every day.

To wrap up this long winded ramble:  2014 was a great year for us, and I can't wait to read about what you guys are working on now!