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.  

pNOVO+

Another example:
pNOVO+ is a new de novo sequencing algorithm that makes use of the complementary fragmentation that we available from HCD and ETD fragmentation.  The authors, Hao Chi  et. al., test their system on peptides derived from a number of different enzymes and demonstrate a staggering level of efficiency.
The paper is available here.
More importantly, as of right now, the link for downloading the program isn't accessible, but it is supposed to be here.  Hopefully it will be up soon!  I can not wait to try it!

This month's JPR is awesome!

You're going to be hearing a lot from me about this month's JPR.  Were they saving up all this great stuff for the New Year?  I'm just kind of floored by how many interesting new studies came out all at once!

2D isoelectric focusing

This month's JPR includes an article by Maria Pernemalm and Jahnne Lehtio at the Karolinska Institutet.  The subject of the study is a new method for performing 2 dimensional isoelectric focusing.  In the first dimension, proteins are separated by IEF.  The strips are then cut, the proteins digested, and the resulting peptides are separated by IEF.  The  team reports a significant increase in their numbers of resolved proteins.
An advantage of this technique over that of the Offgel 2D system is that you don't have to buy the Offgel.  The disadvantage is that normal IEF strips are a good bit more difficult to work with than the Offgel (IMHO).
A schematic of their technique is shown below.

Convert ppm to mmu to dalton

Just another little tool that I meant to move over from the old blog. It is a simple Excel sheet to convert PPM for a specific m/z to MMU and to Da.  John Dalton approves.

Edit -- 5/15/18 -- moved to Google Team Drive. Direct link here.