What an interesting week in the big journals! Nature is running this really great focus on Big Data and what the heck we are going to do with all of it. I think we're all pretty familiar with these problems by now. I am currently carrying...
Sunday, March 31, 2013
Nature special focus on Big Data. Pretty relevant to us!
MaxQuant and QE phosphoproteomics data
This is going to sound more like a gripe than what I mean this to be, but has anyone out there tried to process QE AIF-NL-ddMS2 data with MaxQuant? Holy cow. My server has been cranking at >90% CPU and/or hard drive capacity for 14 hours...
Saturday, March 30, 2013
cBioPortal -- rapid access to numerous cancer genomics sets
Today's issue of Science and Science signaling have a special emphasis on Cancer Genomics. Most of the articles, unfortunately, won't be available to actually read for a couple of days, but I did manage to find something interesting. The...
Friday, March 29, 2013
Culture shock: Proteomics study on CAND1 in Cell makes the news in Seoul!
There is a great proteomics paper in this month's edition of Cell. I spent some time with one of the authors, Dr. J. Eugene Lee, and got an amazing walkthrough on this study where they have identified a protein with a completely novel type...
Thursday, March 28, 2013
LuciPHOr -- phosphosite localization for the TPP
LuciPHOr is one of the gems that I ran into at KHUPO. I spoke to one of the developers and I can't wait to try this out. Upcoming weekend project: same dataset LuciPHOR and the TPP vs Proteome Discoverer 1.4 with PhosphoRS 3.0. Would...
Korea HUPO Day 1
I just wrapped up day one at KHUPO. What did I learn? There is some top-notch proteomics research going on here in Korea. Novel approaches to some old problems, ambitious tackling of some new ones, and some really really nice looking...
Wednesday, March 27, 2013
The ATP-binding proteome of Tuberculosis
Currently in press at MCP is a really cool project that makes amazing use of the Thermo(Pierce) kinase enrichment kits. This paper from Lisa Wolfe et al., represents the work of a group from several institutions and uses the kit to find the proteins...
Tuesday, March 26, 2013
ProteinLasso -- use super statistics to estimate protein interference
There is no art whatsoever on the ProteinLasso website, so I made my own icon with the help of Google Images.Anyway, in every complex MS/MS experiment we ultimately select for fragmentation some ions that we didn't mean to. Increasing sample complexity,...
Is Paris Hilton interning with Steve Gygi?
In a bit of silliness, and something that approximates news (or at least what we seem to consider it in the U.S....) I was looking at the current software offerings from Steve Gygi's lab and was surprised to recognize a face in the lab photo....
Monday, March 25, 2013
Excessive carry-over in your LC-MS system?
This isn't news, just another random topic for discussion (monologue). Here is the question, though: how do you know if you are having excessive carryover in your LC-MS analysis? There are lots of ways to check this, but this is what...
Sunday, March 24, 2013
Q Exactive tutorial for LTQ-Orbitrap users
A while back I threw this video quickly together for a lab with LTQ-Orbitrap experience that had just received their first Q Exactive. It is a quick run-through on how to set up a TopN experiment. It was enough to help them get started before...
Saturday, March 23, 2013
Phosphorylation ends up shifting all over the place?
Ummm....If this was coming out of other labs, maybe I would glaze right over and by this. But this is coming out of Karl Mechtler's lab. Backing up.... A paper in this month's Proteomics (Wiley) from Andreas Schmidt et al., examines...
Beta testers needed! Proteome Discoverer tutorial vidoes
I've been kind of quiet this week. Crazy busy working on my talk for Korea HUPO and this project. A survey following this year's North American iORBI tour suggested that people would be really interested in tutorial videos on our software....
Wednesday, March 20, 2013
ABRF Results 2013
Wow, O.K., this was just brought to my attention in a comment in Sunday's post. This is a big big study of search engines and confident IDs. It is amazing how much can slip your attention in this field. So many cool things go...
Tuesday, March 19, 2013
New article in press -- Identification of Protein Interactions Involved in Cellular Signalling
This new article is currently in press at MCP and comes to us from Westermarck et al., as a collaboration between groups in Turku, Finland at the Institutions whose emblems are shown above. This review takes a very critical look at the technologies...
Monday, March 18, 2013
Proteome Discoverer 1.4 vs MaxQuant 1.3.0.5
A couple of years ago, I wrote a short and blurb on my experience comparing MaxQuant vs Proteome Discoverer. Turns out, it may have been the most read thing I've ever written. If I'd known how many people would read it, maybe I would have...
Sunday, March 17, 2013
It's here!! Proteome Discoverer 1.4
It is here!This week, Proteome Discoverer 1.4 was officially released. Multi-core Sequest anyone? Improved FDR calculations? Spectral library searches? Improved support for Q Exactive data?Wooooo!You can download the demo at the...
Saturday, March 16, 2013
How to set up a binning experiment on an Orbitrap
Recently, we've started doing quantitative experiments by looking in smaller MS1 ranges. But what if you could do discovery based proteomics in the smaller ranges? Would this help your results? Absolutely.This idea has been touched...
Friday, March 15, 2013
Build the ultimate Proteomics Processing PC on a budget
I get this question a lot: How much power do I need to build a PC for proteomics processing? And what components would I need?In order to help answer this I'm going to give the configuration that I would build for processing proteomics...
Thursday, March 14, 2013
Can we quantify a relationship between PTMs and phenotypes?
Here is an interesting line of thought -- can we map the relationship between PTMs and phenotypes? It feels like a big step. As a microbiologist in my past life, we often worked on the link between the genotype and the phenotype. In...
Pittcon update -- Elise Andrew has a booth!
Not really proteomics, just a random awesome thing I got in my Facebook Feed: Elise Andrew, the founder of "I fucking love science" will be at Pittcon giving out shirts and autographs. Don't worry, I'm actually reading literature and have...
Wednesday, March 13, 2013
PITTCON next week
PITTCON kicks off in Philly on Monday, March 17th and runs through the 21st. If you're unfamiliar, it is one of the largest conferences for lab sciences in the world. With a projected 17,000 attendees for this year and nearly 1,000 companies...
Tuesday, March 12, 2013
Refined procedures for studies of ubiquitination --20,000 sites in 1 go!
Another cool paper in MCP this month is this gem from Udeshi et. al., out of Steven Carr's lab. In this, the group reports their strategy and results from a fully optimized enrichment and analysis procedures for anti-di-glycine remnant studies....
Monday, March 11, 2013
Partial explanation of dietary restriction kirunefits?
The picture above is one of a series from the primate longitudinal study that started decades ago. Most of us have seen these. The guy on the left was rather severely restricted in caloric intake, while the inmate on the right was not. They...
Sunday, March 10, 2013
CBTC at University of Toronto is open and looking for collaborators/clients wanting top-notch MS work
After some reorganization, the Center for Biological Timing and Cognition at the University of Toronto was down for a bit. With new management and guidance, is up and fully operational now and looking for clients and collaborators. If...
Saturday, March 9, 2013
Can you use SIEVE for Top Down Data?
I started using SIEVE about 6 months ago. And I feel like I'm finally doing label free peptide quan with grown-ups. Yes, I'm biased, but I never personally cared about lining up my chromatography (and there definitely still are reasons not...
Friday, March 8, 2013
Proteomics of Clostidium toxin effects!
My old pals in the Clostridium world are getting some love in the literature this month!In JPRs papers ASAP, we have a high tech study of the effects Clostridium toxins on cells. The work was done using a SILAC approach on an Orbitrap Velos...
Thursday, March 7, 2013
In depth profiling of the human placenta proteome
In yet another amazing paper out of our friends at the human proteome project, this new paper from HJ Lee et al., describes the comprehensive proteomic mapping of the human placental proteome. Maybe we overuse the word "comprehensive" sometimes....
Big Month for Label Free Quan -- 2 new reviews!
In case you're looking for a new review on label free quan, this month you are in luck. Both this month's MCP and this month's Proteomics (Wiley) feature reviews on the topic.The article in Proteomics is from Matzke et al., out of PNNL and can...
ChemCalc -- Exact mass calculator
Whenever you get tired of all the drivel that is on the internet, take a step back and look at all the awesome services there are out there. The UCSF Protein prospector has been out there forever and is just awesome. How many of us still...
Wednesday, March 6, 2013
SweetSeqer: Glycopeptide analysis software!
More magic from the Steen and Steen lab! In press at MCP is this paper from Serang et al., that details a new software package called SweetSeqer. This uses a de novo type approach to evaluate glycopeptides. For any of you guys doing...
Tuesday, March 5, 2013
Spec&SepNow a pretty App you can't log into
I got a notice from the Apple Genius thing that said spectroscopy/separationsNow.com had a new app. This would work similar to Sparkplug, where it would provide me with abstracts that met one of many criteria that I set for upcoming literature...
Korean HUPO 2013
The KHUPO conference is the 28th and 29th of this month in Seoul. The highlights for me? Top notch researchers like Akhilesh Pandey, Mike MacCoss, Michael Freeman, and William Hancock. Another big one for me is Henry Rodriguez who will...
Monday, March 4, 2013
Xcalibur 64-bit
This doesn't come from the Xcalibur that I mean, it is just a little cooler looking. It appears to be from some Casino gambling game. This is just a quick blurb in case you didn't know that a 64-bit version of Xcalibur is available. In December...
Subscribe to:
Posts (Atom)