Tuesday, December 31, 2013

New methods in Orbitrap methods database

Recently, I've gotten to be in on a couple of Orbitrap Fusion installs and got to play around a little with different samples.  I've uploaded some methods that have produced nice results to the Orbitrap methods database.  The first is an MS2...
READ MORE - New methods in Orbitrap methods database

Monday, December 30, 2013

Proteome screening of pleural effusions identifies galectin 1 as a diagnostic biomarker and highlights several prognostic biomarkers for malignant mesothelioma.

Mesothelioma is a cancer that starts in the protective lining around your organs.  Since the massive removal of asbestos in North America over the last 20 years or so, we rarely hear about this cancer now, as it was the major cause.  Asbestos...
READ MORE - Proteome screening of pleural effusions identifies galectin 1 as a diagnostic biomarker and highlights several prognostic biomarkers for malignant mesothelioma.

Sunday, December 29, 2013

Most active Twitterers in Proteomics

Oh, Lists! Why do we love you so much?In another example, Google+ suggested this article for me regarding the most active Twitterers (I don't think that is the best diction, but you probably know what I mean) in our field.  I follow most of these...
READ MORE - Most active Twitterers in Proteomics

Tuesday, December 24, 2013

Backdated --- Merry Xmas!!!

I took a break from the blog for the holiday but this picture is too awesome to not use ...
READ MORE - Backdated --- Merry Xmas!!!

Monday, December 23, 2013

Use of quantitative mass spectrometric analysis to elucidate the mechanisms of phospho-priming and auto-activation of the checkpoint kinase Rad53 in vivo

Rad53 is a protein that is involved in DNA repair in yeast.  An extremely similar protein in humans, Rad51, is shown above.  You irradiate some cells and probe with an anti-Rad51 antibody and you get the distinct foci shown in green above.Despite...
READ MORE - Use of quantitative mass spectrometric analysis to elucidate the mechanisms of phospho-priming and auto-activation of the checkpoint kinase Rad53 in vivo

Friday, December 20, 2013

Mass spec terminology translator V1 is up

I have no idea what is happening in the image above.  GoogleImages gave it to me when I said "pug translator". Anyway!  As long promised I finally put up the first version of the mass spec terminology translator (see top right).  This...
READ MORE - Mass spec terminology translator V1 is up

Mass spec free proteomics!?!?!

Lets start off like this:  This is a paper in MCP but they didnt do any mass spectrometry, not even a little, so why do we care?Next article please!No, wait!  This is awesome, I promise. You know how I'm always preaching that the database ought...
READ MORE - Mass spec free proteomics!?!?!

Thursday, December 19, 2013

Do Byonic searches directly in Proteome Discoverer!!!!!!

I knew this was coming.  I really really did.  But that doesn't stop me from being crazy super psyched about it.You can buy a Byonic node and put it directly into Proteome Discoverer right now!If you don't know about Byonic, go to the search...
READ MORE - Do Byonic searches directly in Proteome Discoverer!!!!!!

Wednesday, December 18, 2013

Quantifying protein interaction dynamics by SWATH mass spectometry: application to the 14-3-3 system

A recent article in Nature Methods describes a very nice study on mapping protein-protein interactions using mass spectrometry.  The proteins of interest are the 14-3-3 family of generic scaffolding proteins.  The MS method used is a data independent...
READ MORE - Quantifying protein interaction dynamics by SWATH mass spectometry: application to the 14-3-3 system

Tuesday, December 17, 2013

Rockethub -- Another place to crowdsource fund some science

This article came by way of this month's Wired (which is pretty great, btw, as Bill Gates stepped in as editor).  I knew about RocketHub, but I didn't realize that people were successfully using this as a method to fund their research.  You...
READ MORE - Rockethub -- Another place to crowdsource fund some science

Monday, December 16, 2013

Tools for proteomics app

This is a neat little app.  Visually appealing and with nice little summaries of mass spec techniques and hyperlinks to where you can actually purchase the consumables to do the work.  Now, how many people have purchasing departments that will...
READ MORE - Tools for proteomics app

Sunday, December 15, 2013

Matching cross-linked peptide spectra: only as good as the worse identification

We all want to cross-link peptides and do mass spec on them, right?  We have a protein of interest and we want to know what other proteins are interacting with it.  So the strategy is to throw in one of the 20 or so crosslinkers out there,...
READ MORE - Matching cross-linked peptide spectra: only as good as the worse identification

Saturday, December 14, 2013

Spectral counting in Proteome Discoverer

The image above is stolen directly by/from Google Images.  First thing that pops up if you look up "spectral counting".  Anyway, I often get questions about using Proteome Discoverer for spectral counting.  I have some slides that I cut...
READ MORE - Spectral counting in Proteome Discoverer

Friday, December 13, 2013

Peaks 7

My first Xmas present arrived while I was on vacation.  Peaks 7 came out and I got a nice long trial license to check it out.  I installed it on my plane ride home.The list of new features from Peaks 6 to Peaks 7 is kind of mind blowing.  This...
READ MORE - Peaks 7

Thursday, December 12, 2013

MaConDa -- A nice resource for identifying contaminants

This is a cool resource I recently stumbled across!  The MaConDa is a really easy and simple site that has exact mass information on previously identified contaminants in MS/MS runs.  I know most of us have the supplemental information Excel...
READ MORE - MaConDa -- A nice resource for identifying contaminants

Sunday, December 8, 2013

GOrilla -- Gene ontology tool with a great name

Quick note that I found while reading the new MCP on vacation...I know....I have a problem.  In my defense, there are some great papers this month....Anyway, a new to me tool for gene ontology is GOrilla, which appears to be hosted by the Weizmann...
READ MORE - GOrilla -- Gene ontology tool with a great name

Friday, December 6, 2013

Ohaiyou gozaimasu!

Ive got one backpack full of stuff, my IPad, and I'm on a bus to the mountains of northern Japan.  My goals include seeing a wild snow monkey, snowboarding, and making a dent in the global supply of Sapporo (which is crazy cheap here!).  As...
READ MORE - Ohaiyou gozaimasu!

Thursday, December 5, 2013

PRTC. I swear I wrote this entry once before!

Are you running some sort of quality control when you do proteomics?  If your answer is "of course" then I like you.  Heck, I'm a friendly guy.  If your answer was "never, and I hate pugs!" I'd probably still like you, but I might like...
READ MORE - PRTC. I swear I wrote this entry once before!

Wednesday, December 4, 2013

Comparison of peptide and protein fractionation methods in proteomics

This is a nice analysis that comes from a pretty simple set of experiments that were just done nicely.  The article from Mostovenko et. al., (open access!) compares multiple methods of fractionating both an E.coli digest and a single digest...
READ MORE - Comparison of peptide and protein fractionation methods in proteomics

Tuesday, December 3, 2013

Protein Expression Control Analysis (PECA)

This is a paper for all you bioinformatics people out there.  Partially because you need to have a stronger background in computer stuff that I do to even install and use PECA.It appears to be a nice tool for the analysis of RNA expression data...
READ MORE - Protein Expression Control Analysis (PECA)

Monday, December 2, 2013

Arginine phosphorylation in bacterial stress response

In press at MCP is a great new paper showing how arginine phosphorylation is used by Bacillus subtilis in the regulation of response to stress. And it isn't a little involved.  It's a lot involved.  This study shows that it can be linked...
READ MORE - Arginine phosphorylation in bacterial stress response

Sunday, December 1, 2013

How far is the human proteome project at this point?

The human proteome project has been rocking for a while now.  How far has all this work gotten so far.Well, here is an update (not open access), compliments of JPR and Terry Farrah et. al., and the number is around 62%. 62% what? Oh, 62% of the...
READ MORE - How far is the human proteome project at this point?

Saturday, November 30, 2013

Comprehensive history of the Orbitrap by Dr. Makarov!

There are a lot of stories out there about the development of the Orbitrap system.  Want the whole story directly from Alexander Makarov?  Check out this month's issue of the Analytical Scientist, cause he wrote out the whole history.The article,...
READ MORE - Comprehensive history of the Orbitrap by Dr. Makarov!

Friday, November 29, 2013

How does TMT10 affect peptide charge states?

A reader wrote in with this very sensible question regarding one of my posts on the TMT 10plex reagents.  The question from Javi:  How does the new TMT 10plex reagent affect peptide charge states.  For example, he notes, that iTRAQ can...
READ MORE - How does TMT10 affect peptide charge states?

Thursday, November 28, 2013

Turkey (egg shell) proteomics!

Happy Turkey day!  This time, that isn't my pug, he just looks just like him!  That costume is ridiculously expensive.  I'll get it after the holiday when it goes on sale for next year!Now, I often wonder strange things like:  A whole...
READ MORE - Turkey (egg shell) proteomics!

Wednesday, November 27, 2013

What does a good TMT or iTRAQ MS/MS spectra look like?

Holy cow!  I haven't posted anything in almost a week.  Normally there are very good reasons for this, like 1) I changed my password and forgot it or 2) It was nouveau week, or 3) The super cool projects I'm working on in my spare time are...
READ MORE - What does a good TMT or iTRAQ MS/MS spectra look like?

Thursday, November 21, 2013

SCAMPI-- A statistical approach to protein quantification

We need more statistics in proteomics.  We all know that.  We particularly need them in our quantification studies.  This is a little easier when we're doing label free but, of course, that comes with its own set of new challenges. I get...
READ MORE - SCAMPI-- A statistical approach to protein quantification

Wednesday, November 20, 2013

How to do intact or top-down analysis of intact proteins on an Orbitrap

It is funny that I haven't written about this before, particularly when it is such a common question for me to be asked, and even more particularly because it is so counter-intuitive.First of all, I don't understand the physics or anything, I just have...
READ MORE - How to do intact or top-down analysis of intact proteins on an Orbitrap

Can't get those last air bubbles out of your nano-LC system?

So you've purged and flushed air, and ran your LC at high speed, but you've still go some pesky airbubbles eluting from the tip of your emitter?  Don't just get super angry, do something about it!I just learned this trick this week after spending...
READ MORE - Can't get those last air bubbles out of your nano-LC system?

Tuesday, November 19, 2013

Shortix: Cut silica correctly every time!

A group I'm working with this week has this awesome little tool.  It is perfect for people like me who can't cut fused silica cleanly and evenly any every single time they try.You push the silica into the device while repressing a little entry button...
READ MORE - Shortix: Cut silica correctly every time!

Monday, November 18, 2013

IPRG 2012 -- What did we learn?

IPRG 2012:  What did we learn?In general, the ABRF (The Association of Biomolecular Resource Facilities) has some awesome ideas and the IPRG 2012 study is no exception.In this study, synthetic peptides were produced that contained common modifications...
READ MORE - IPRG 2012 -- What did we learn?

Saturday, November 16, 2013

Nerdy computer note of the month: DDR4 release!

PC nerd alert.  DDR4 memory is about to release.  Crucial says they'll have the first modules out next month.  Want your processing PC to access memory faster, but also use less energy?  Enter DDR4.  Twice as much memory per...
READ MORE - Nerdy computer note of the month: DDR4 release!

59 proteoforms of ovalbumin?

I'm currently just overwhelmed in my raw appreciation of just how cool science is and of how very very little we seem to know about our world around us.  There is stuff to discover absolutely everywhere! Case in point, this new paper out of Albert...
READ MORE - 59 proteoforms of ovalbumin?

Friday, November 15, 2013

Weak statistics and lack of reproducibility

Umm...this one is disturbing.Let's start at the title:Weak statistical standards implicated in scientific irreproducibilityand then move to the subtitle:One-quarter of studies that meet commonly used statistical cutoff may be false.Ummm...already disturbing,...
READ MORE - Weak statistics and lack of reproducibility

Thursday, November 14, 2013

Poo proteomics!

It is probably a little immature that I'm taking this very serious, interesting, and well published study and reducing it to the term "poo proteomics."  But sometimes, that just happens, and it's still my blog (please refer to disclaimer page)!...
READ MORE - Poo proteomics!

mMass -- easy open source tools for mass spectra

I just happened across this one when 2 people asked me about a nice open source in silico fragmentation predictor in the same day.  Sounds like search that will end up as a post!I looked around, downloaded a few, and found my favorite, and it is...
READ MORE - mMass -- easy open source tools for mass spectra

Wednesday, November 13, 2013

Uniprot update available today

Uniprot update time!  Last update of 2013.  Update he...
READ MORE - Uniprot update available today