Sunday, June 3, 2018

The Skyline User meeting recap!

The Skyline User Meeting was 🔥🔥🔥🔥🔥🔥 (I'm not sure what that means, but context clues from Twitter and Reddit suggest to me that I'm using it right).

How do you have a successful user's meeting for awesome open source software?  Maybe you have it in an amazing old public library -- you get support from vendor sponsors to provide really good food, and -- most importantly (of course) -- maybe you stack a ton of talks on things that we didn't know this great software on our desktops could even do!!  Even though a vendor had offered a free cruise of the harbor for lunch -- enthusiastic Skyline users filled this less flashy event.

Talk 1: Chris Ashwood of Medical College of Wisconsin (and Head Editor of Glycomics Methods for

Glycan analysis and characterization with Skyline! The first paper came out recently, but he showed that this might be the tip of the iceberg. Even better maybe? What about a fully developed internal/QC standard? For glycomics? Yeah!

Talk 2: Paul Auger at Genentech

Automated QC with Panorama for peptides AND small molecules!! Okay. I knew Panorama was out there. I knew that Mike Bereman's work with sProCoP had been integrated entirely into Panorama. What we didn't know? That you can set up a local Panorama server (in case your instruments aren't accessible to the outside world!) and get all the benefits of Panorama inside your network!

Benefits like: real time QC/QA on ALL of your instruments.
Know that ion transfer tube is gonna need a new one dropped in --- before you're 2SDs low on sensitivity!   This talk required an email to our director (we need him to buy us a server so we can put Panorama on it)

Talk 3: Robert Ahrens -- LipidCreator/LipidExplorer + Skyline!!

Have you even heard of this?  This open(?) lipid software looks ridiculously powerful and the developers got in touch and now its a Skyline powered quantitative lipidomics platform!  Is there anything better than adding new applications to a piece of software you already know really well? Sure, you'll need to learn something new -- but you aren't starting from scratch and that gives you a massive lead on getting that application going in your lab!

Talk 4: Don Davis of Vanderbilt and developing Clinical Assays in Skyline!!!

This was a great lightning talk where the real consequences of the implications of the work this team at Vanderbilt is doing didn't really hit me until about 3 minutes into the next talk. For a lot of us, our end goal is new biomarkers or diagnostics -- and Don showed how feasible moving what you've developed in the lab could really be -- without the added complication (again0 of having to learn something new. With Skyline piling on new Auditing features (which Brendan assures us you can actually see -- just not on a projector 😜) why not? If all the necessary security protocols are in place -- why couldn't we develop an assay and just port it right into the clinic -- without having to re-optimize with new software??

Talk 5? Yao Chen from Catalent -- what about antibodies?!?  

Heck, why not. Why not use Skyline as a (digested) antibody characterization system?! Apparently it can do everything else. There are some really important reasons to use more targeted approaches for mAB characterization, but I've been trying to pull his references and I'm not sure what has been published, so I'm gonna stop that one here.

Talk 6? Kristen Geddes from Merck -- Panorama QC of a diverse portfolio of instruments doing all sorts of things.

If Conor and I weren't already sold on Panorama -- seeing this great talk -- Merck isn't a single vendor kind of place. Their LC and MS systems aren't even single vendor -- but QC with was shown to be powerful and well automated with a local instance of Panorama handling the whole thing! Yeah -- we need to get this set up.

Talk 7? Buyun Chen from Genentech -- taking a deep look at peptide and protein quan. 

Again -- Buyun gave a great talk, but I'm not sure how much has been published. She raised some really important questions (with some solid data) about peptide and protein quan -- and how Skyline can really help you find those peptides that TRULY reflect the amount of the proteins present. Some basic fundamental questions are being explored and if I see that this work is published, it's going to end up here for sure.

Talk 8? Lindsay Pino  SIGNAL calibration in quantitative proteomics. 

I think this is being written up (maybe I'm just being lazy) so I'm not going to go into it much -- but -- what if you could do a PRM on your Orbitrap Elite AND compare it to PRM on your Orbitrap Fusion (I'm using this because it's an extreme example -- I often get areas >1e11 on the Elite -- I don't think numbers that big can be displayed on the Fusion -- Signal calibration is something we're going to be talking about in the future -- Lindsay demonstrated with some amazingly diverse datasets that 1) Signal calibration is critical and 2) She can show us how to do it.

Wrap up:

Brendan MacLean filled in some interesting history on the almost 10 years of Skyline -- where it is -- and where it is going next.

Worth noting, maybe -- due to some rearrangements in the grant process -- (NIGMS no longer has a separate category for software like Skyline. The grants supporting this software are going to need to be fully competed (against things that aren't software). User feedback to the grant review boards and the vendors who chip in to support the process will likely become more important as time goes by. Not to end on a downer -- this was an AWESOME workshop -- but I'm sure it would be easier for the developers if the 10,000 of us that have this software had each paid $15,000 for it. So it's worth keeping in mind we may have to do surveys once in a while to keep Skyline free, and open and improving.

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