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.

Correlation between iTRAQ reagent sets

A new study in this month's JPR takes a look at the correlation between 2-plex and 6-plex iTRAQ reagent kits. The results are a bit surprising to me, but they two reagent kits show a pretty strong correlation.
You can find this study from Rauniyar et. al., here.
Below is an overview of their experimental design.

Protein Deconvolution Estimator

This is one of those things I posted on the old blog a couple years ago and kept meaning to bring over to this new one.  It is a simple Excel spreadsheet for estimating the deconvoluted mass of an intact protein.  It certainly isn't perfect (+/-1000 Da?), but it is better than what you'll find if you Google "free protein deconvolution," which, last I checked, comes up with nothing.  If you use it, I just ask that you aren't a jerk about it.  ;)
You can download it from my personal bytebuckets account here.

BaseSpace cloud genomics computing

Again, not proteomics.  I may need to re-name this blog soon.  Anyway, BaseSpace cloud genomics is a service from Illumina that is set to kick off in January.  It is an attempt to use brute strength to solve the difficulties of dealing with large amounts of genomics data.  Typical genomics experiment on a dedicated power PC:  design experiment (20 minutes) run experiment (24 hours) find typo in experiment and fix (1 min), rerun (24 hours), etc.,  and this was my experience with around 50 GB of microarrays.  These next gen files can be substantially bigger than even the newest human Affy chips.  By using a cloud computing format, each manipulation will be reasonably quick.  Now we just need dedicated proteomics cloud computers!
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