Sunday, September 22, 2013

Elsevier Connect -- Publishing articles becomes more sophisticated


Publishing an article has always been kind of a black box.  They accept your paper and, in most cases, you are left with little indication of how your work was received.  Considering how much information is at our fingertips in every other way, it is a little strange.  For example, I have a dashboard that tells me how much my readers appreciate what I write.  I get a real time tracker that shows me what articles are being read, when, and from what geography.

In contrast, I have no idea if anything I've ever published in a peer-reviewed journal has ever been cited.  I'd guess it probably hasn't been, but how would I know without digging for it?

Elsevier connect is trying to pull back the blinds a bit to let you see the fate of your Elsevier accepted article, by providing just that kind of information.  Definitely worth checking out, especially if you're trying to shape that career.  You can read more about it here.

Tuesday, September 10, 2013

DMSO improves shotgun proteomics?


I was reserving my opinion on this because it sounded just a little crazy, but I heard yesterday that this study has been replicated by another group.  Spiking low levels of DMSO into your LC-MS shotgun proteomics experiment appears to have fantastic effects on your signal intensity and your coverage.
Does it make sense to me?
Nope.
Do I know what kind of effect this will have on LC-MS/MS systems?
Nope.
CAUTION (AND DISCLAIMER):  Some LC components, particularly proteomics centric nanoflow systems possess chemically sensitive seals that are optimized for formic acid and acetonitrile only.  Consult your owner's manual and/or LC applications team to see if your LC-MS system can handle this buffer additive.  I am seeking insight from different LC vendors to see what they're opinion on this is and/or which systems are compatible.

Am I going to try this as soon as I possibly can?

I'll get back when I have solid data (2-3 weeks, probably...)  For now, however, check out the original method paper here.

Friday, September 6, 2013

Humble beginnings for the Orbitrap methods database


I have been on the road pretty consistently since my last post (and will be for a good bit longer), so this fell by the wayside.
But, I finally got some Orbitrap methods uploaded.  At this point, I'm just going through my old RAW data and finding methods that produced really good results and copying the text into Word.

So far, the list consists of a decision tree based ETD method for an Orbitrap XL plus ETD, a Top20 CID method for an Elite, a Top15 method for a Q Exactive and an AIF-based phosphoproteomics method for the Q Exactive.

More will follow.
Disclaimer (#7?):  These aren't perfect.  They are simply meant to be good starting points for you if you are new to these instruments or are trying a new application.  My employer's, past present or future have nothing to do with this. Good luck!

The Orbitrap methods database!


Tuesday, September 3, 2013

IonSource -- Another great online MS resource


I'm sure everyone already knows about IonSource.  It appears to have been around forever, but that doesn't mean that I would know about it (how many resources do we have out there!??!)
Great site with tons of info.  I strongly recommend you check it out when you have time.

Direct link here.