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,...
Saturday, November 30, 2013
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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,...
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)!...
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...
Wednesday, November 13, 2013
Uniprot update available today
Uniprot update time! Last update of 2013. Update he...
Open source tools for top down proteomics
Want to do some top-down data processing on the cheap? Are you willing to write a command line here and there and jump through a data conversion hoop or two? Then there are a couple of tools that will work for you or the bioinformatics guy...
ItunesU free courses in mass spectrometry
Aside from the crazy randomness of the internet, my second favorite thing about it is the easy access to information about everything. Suddenly fascinated by the fact that gel nail polish is polymerized by placing the customer's nails in a UV light...
Tuesday, November 12, 2013
iPRG 2013 -- Next gen sequencing + proteomics!
In my humble opinion, proteomics is just on the verge of going into full-out revolution. We keep hinting at it with the "dirty genomics" idea and a few studies here and there that have shown the potential of searching MS/MS spectra against "next-gen"...
Monday, November 11, 2013
Transferred subgroup FDR for rare PTMs
A new paper currently in press at MCP takes a novel approach at calculating the false discovery rates of post translational modifications. The work, from Fu and Qian, researchers at two facilities in Beijing, tries separating out FDR for modified...
Sunday, November 10, 2013
What kind of fish is it?
Counterfeiting food is a surprisingly big problem in first world countries these days. (Problems that I'm sure seem pretty minor to people on the other side of the developing/developed boundary...) The problem was highlighted on a segment...
Saturday, November 9, 2013
Is protein denaturation the key to the serum proteomics?
Serum and plasma proteomics experiments suck. They just do. With modern instrumentation you can take a cell pellet from just about anything and knock out an easy 2,000 plus unique proteins. But then someone brings you some plasma or...
Friday, November 8, 2013
MSAmanda, Sequest, Percolator discussion part 2
This is a continuation of a previous analysis from last week. Part 1 is here.Okay, here is the question. What, if anything, is MSAmanda giving us that we aren't getting from Sequest + Percolator? In the previous entry I think I did...
Thursday, November 7, 2013
Fame in science
Uh oh! This one has been percolating in my head for a while. Do I write it and risk offending a lot of really smart people? Or should I just do some vinyasa flow and just let this negative energy drain into the cosmos? In the...
Wednesday, November 6, 2013
What is a TopN Peaks filter?
One at a time, I've been going through the PD nodes, new and old and evaluating them in exactly the way that one should. Using my current favorite dataset, I simply add in the new node and run the same sample with and without this node. It...
Tuesday, November 5, 2013
OpenMS -- new algorithm for metabolomics
In press at MCP right now, is this paper: "Automated Label-Free Quantification of Metabolites from LC-MS Data," by Erhan Kenar et al.,Now, I know this is a proteomics blog, but I try to keep my ear to the ground in regard to this metabolomics...
Monday, November 4, 2013
Does our target threshold for MS/MS actually matter?
This very thoughtful question was recently posed to me by someone. And I had a nice long think about it on a plane today.Here it is: If we are always going for our most intense ions, Top10 or 20 or whatever, would it even matter what we put...
Sunday, November 3, 2013
Dynamic exclusion -- which camp are you in?
I've noticed in my traveling that there are 2 very distinct ways that people set up their dynamic exclusion settings. I've taken to referring to them as the two camps. Here are some really crooked illustrations with somewhat arbitrary and...
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