SprayQC -- take the guesswork out of nanospray!

I talk about this paper so often that  I was certain I had written about it.  SprayQC is an open source software program from Richard Scheltema and Matthias Mann that aims to provide easy computer monitored analysis of your nanospray.  It requires a bit of hardware, including a new camera and video card for your PC ($100?) and is absolutely worth your time.
 Picture this:  Middle of the night and your deep into fraction 7 of these tumor digests and your spray goes all wonky.  Normally, you get in the next morning and it ruins your day.  Sample lost forever.  But if you have SprayQC and your spray goes wonky?  The runs stop.  And by wonky, I mean that it is using a video to monitor your spray stability in real time, it also monitors your LC system for errors and it monitors you TIC baseline for weirdness.  If these occur, SprayQC stops after your run and then sends you an email describing why and how the run was stopped.  In my opinion, everyone should have this software installed on their PC. It was written with the EasyNano and the NanoFlex source in mind, but it is easily adaptable to other LCs and nanosources.
You can read more about this fantastic program here.

Comet search engine -- free multicore Sequest?

Comet is the topic of this new paper from Jimmy Eng et. al., and it appears to be a search engine based on the original Sequest algorithm.  It has been adapted to be multi-threaded so that it can work on multicore PCs.  There are some caveats, however, to this (as well as most) free stuff.  The first is that there currently is no GUI (graphical user interface), you'll have to write one yourself.  The alternative is that you will have to order your searches using a command line (DOS, for us old guys) which will get very tiresome.  It also doesn't appear to be 64-bit compatible.  It is definitely nice that it is out there, but you will have to do a little work to get it where you want it.  I do like the icon.  It's blown up here because I couldn't find a higher resolution graphic, but it looks nice on a desktop.

Proteomic snapshot of breast cancer cell cycle: G1/S transition point

When DNA damage occurs in normal cells, the cell development/division cycle will stop at the next of several checkpoints that occur throughout normal progression.  The cell will stay at that point until the damage can be repaired.  If the damage can't be repaired the cell will never leave that checkpoint and won't divide again.  If the damage is extreme, the cell may voluntarily self-destruct through the process of apoptosis.  Cancer cells, however, will just shoot through these checkpoints and keep dividing regardless of the amount of DNA damage present.
How and why a cancer cell does this is the focus of this new paper from Milagros Tenja and (a member of my thesis committee) Iulia M. Lazar.  In this study they look at the breast cancer cell line MCF-7 and perform label free quan using spectral counting to identify pathways that are involved in enriched nuclear and mitochondrial fractions.  The paper is a featured article of this month's Proteomics, so you should check it out.  Go Hokies!

PBI Shredder -- use pressure to extract your proteins?

I recently read about this instrument in The Scientist.  It is a permutation of your basic homogenizer systems.  While I'm not completely clear on its mechanism of operation, what I do get is that it uses a finely adjustable pressure to lyse cells with minimal shear pressure.  While it is marketed primarily for DNA extraction, the producers do mention that it can be used for proteins.  While it would probably have limited usefulness for most of us shotgun MS/MS people, particularly the membrane centric ones (like me!), I could see where it could be useful for others.  This might be a great way to get proteins out for top-down analysis of protein complexes, as sonication does tend to damage larger proteins more, who knows what it does to large protein complexes (probably bad things!).  You can read more about the PBI Shredder at the manufacturer's website, as well as watch a video!

StavroX -- software for disulfide link analysis

This paper is a little older (2011) but just recently came to my attention.  The study, by Gotze, et. al., details the construction and testing of StavroX a software package for studying enzymatically linked peptides with intact disulfide bridges.  Following the development, the authors go on to show that the software works with three different biological systems.  If you are interested in protein-protein interactions, you might want to check this out!

Does Hyper threading work in proteomics applications?

This is an interesting thing that recently came to my attention.  Does "hyper" or "virtual" threading actually work in Proteomics applications?  In at least one instance I've seen evidence that it does not.
What is hyperthreading?  It is a virtual processing unit used by Intel processors that enables tasks to be performed while one core is not busy.  Here is an illustration I stole using  Google Images:

The gist is this:  In normal applications using multiple processing cores, sometimes one core isn't doing anything.  When that occurs, hyper-threading goes ahead and runs the next processing thread.  In most applications, this allows the CPU and motherboard to pretend they have additional cores.  This runs on the assumption that there will be dead time for the cores.
This is where the problems comes in with hyperthreading and proteomics data processing:  when you're running a search algorithm on a huge proteomics file, the cores never get a chance to take a break -- or at least very rarely.  With no stop in the processing on-slaught, the processor that is pretending to be an 8 core processor, is the 4 core it really is and no advantage is gained from pretending.
Keep in mind that this is from an extremely limited experiment but:  a comparison of an Intel processor with 4 cores and hyperthreading enabled to an AMD 8 core processor came up extremely different than one would predict when comparing their rankings on the Passmark CPU benchmarking chart.  The Intel processor in question was ranked considerably faster by benchmark but was absolutely smoked by the 8 core PC although Passmark's study had shown the AMD was less than 70% of the speed of the Intel processor.  Again--limited experiment, but when the Intel processor in question was almost 10 times as expensive as the AMD, it makes you want to try it out yourself, right?
 I'd love to hear from other people who have data on this!

Proteois: FDR for label free quan!

Currently in press at MCP is this paper from Marianne Sandin et al., that describes Proteois, and adaptive alignment algorithm for label free quantification experiments.  An interesting aspect of this algorithm is the use of a false discovery rate (FDR) calculation during the alignment stages.  Another nice feature is that there are multiple readouts during the alignment and quan steps that allow you to rapidly troubleshoot problems with your analysis.

ASMS 2013 Deadline is rapidly approaching!

It is January 10th people!  Less than a month left to get your abstracts in for ASMS 2013.  Don't miss your chance to show off your work in sunny Minneapolis!

iPathways

iPathways is a program available through the App store for iPhone and iPad that catalogs biological pathways.  The pros are that the App is really fast, since the pathways are images rather than changing objects.  The downside to this particular App is that each pathway is so extensive that you have to pinch and drag an awful lot to move around the image.  Is it as good as a searchable manually curated database such as Protein Center?  Definitely not!  But is it useful?  Absolutely.  And don't take my word for it, this App has over 6,500 other registered users.

iCOPa Heart Proteome Database App

Happy New Year!
For anyone doing proteomics on heart tissue -- there's an App for that!  The iCOPa is a curated database of proteomics data that has been stored.  Unfortunately, I can't really speak to the ease of use or efficiency, because I don't actually have any heart tissue proteomics data to filter it with, but it's a great idea nonetheless!
It is linked to the data of the cardiat organella protein atlast knowledgebase, that you can learn more about here.