I seriously have a list of the next 10 things to investigate/write about, but this one just hopped the queue. If you haven't noticed, I'm doing a lot of crosslinking stuff right now. The MS/MS and data analysis is tricky stuff. Yesterday,...
Monday, March 31, 2014
Sunday, March 30, 2014
Byonic in Proteome Discoverer
Byonic time!As I mentioned earlier, one of my favorite MS/MS programs ever, Byonic, has been seemlessly integrated into the Proteome Discoverer 1.4 environment. If you haven't heard of Byonic, I wrote a couple posts on it over the last 2 years....
Peptide Shaker!
Y'all are always coming up with so much cool stuff! Peptide Shaker isn't exactly new, but its mostly new to me. Heard of it, but I never went out of my way to check it out. It is real cool. Not only do you get a nice (and interesting...
Saturday, March 29, 2014
Preview in Proteome Discoverer
I have SO much to write about right now. Its killing me that I have this real job that I have to do. This one is going to be kind of short cause today is pretty packed. Preview is a program from Protein Metrics that quickly evaluates your...
Friday, March 28, 2014
Quantitative analysis of 4000 proteins on a QE!
I have so much to write about right now! March is a great month for proteomics!First off, thanks @pastelbio for letting me know about this great new paper in Nature Scientific Reports.This paper (open access) from Liangliang Sun et al., uses iTRAQ...
Thursday, March 27, 2014
Getting beyond parsimony
Wanna feel dumb sometime? Pick up a paper with Oliver Serang listed as an author. But its important, very very important that we start thinking about the things he has been thinking about, because what Oliver has been working on is our problems...
Wednesday, March 26, 2014
Quality control in Skyline!
Man, I'm gonna get sued for real one day. But this is the best image I can think of to describe this paper, because we're combining two of my top 10 mass spec things (don't ask for the complete list, its probably really weird) -- Quality control...
Tuesday, March 25, 2014
Check out the new Software Portal
I don't know when this changed, but it had to been recently. The BRIMS Thermo Omics Software Portal has been totally rebooted. It looks great and it is even better organized!...
Free genomics classes from Harvard
Another great contribution from a super cool person!Want to know about genomics, including the "next gen" stuff we keep hearing about? You should consider taking a free eLearning class from Harvard. How badass is that? Seriously? If...
Monday, March 24, 2014
PTMrs!!! Confident site localization of all PTMS in Proteome Discoverer!
WOOOOOOOOHHHOOOOOOOO!!!!I have yet another awesome new node that you don't have! If you are interested in any kind of PTM, you are going to want this.You know PhosphoRS. Site localization probabilities for your phosphorylation events. Last...
Saturday, March 22, 2014
SILAC label a whole fish, cause why not?
Do you love working with zebra fish, but are frustrated by how little proteomics has been done on your favorite model organism? Marcus Kruger's lab at the Max Planck Institute finally said "enough is enough" and labeled the whole damned fish. Using...
Thursday, March 20, 2014
Mash Suite
The other day I joined that ASMS thing y'all are always going on about. And I'm already reaping the kirunefits. I got a journal in the mail with a ton of articles and I didn't have to worry about whether they were open source or not, cause...
Wednesday, March 19, 2014
Phosphoproteomics of hallucinations?
I'm fascinated by these brain proteomics papers. How much functioning in the brain can we detect by shifts in post translational modifications? It sure seems like a lot!In this paper (in press at MCP and temporarily open access) from Karaki...
Tuesday, March 18, 2014
Byonic node for Proteome Discoverer
Look what my nice friends at ProteinMetrics gave me to test out! My favorite engine for searching MS/MS data for post translational modifications directly ported into my favorite proteomics processing software! I'll be back later with tests and...
Monday, March 17, 2014
Quan on the QE Part 4: Data independent acquisition
Haven't read the rest of it? Here is part 1This is part 4 of my monologue on (what I was calling targeted) quan strategies for the Q Exactive. Last week someone told me that he never says the full name of this technique to collaborators...
How people respond to data.
I was sent this link this morning and had to share it. How people respond to data.Don't worry, I really am going to do the DIA post soon! If I didn't post silly stuff once in a while, a lot of your would probably stop following me, and you know...
Sunday, March 16, 2014
Chemistry lab suite app
(Image stolen from Bah Humpug!)With the rise of the mobile device, everyone in the world is exploring how to make these powerful little computers we're carrying all the time even more useful than they are. Two Apps that I use a lot are SparkPlug...
Saturday, March 15, 2014
The rise of OpenProteomics?
Are we starting to get organized as a field? Check out this awesome press release from EMBL!Thanks @attilacsordis for the heads up on this one. We're making steps in the right direction all the t...
Friday, March 14, 2014
Targeted quan on the QE part 3
Welcome to my monologue on the many methods for targeted quan on the Q Exactive. Yes, I honestly took the time to make a Super Saiyan Q Exactive. No, I don't know what is wrong with me. Yes, I'm starting to worry.Check out part 1 hereAnd...
Thursday, March 13, 2014
Targeted quan on the QE part 2!
Yay! Part 2!Check out Part 1 here. The response has been...enthusiastic. I didn't know so many triple quad users read my blog!Next on my list is plain old, MS1-ddMS2, with an Inclusion ListCouple of different ways we could process this....
Wednesday, March 12, 2014
Targeted quan on the Q Exactive -- Which method to use when? Part 1
One of the many things the Q Exactive is good (great?) at is targeted quan. But it can be a little tricky. You have a ton of different methods to choose from for doing targeted quan and each has advantages /disadvantages over the others....
Tuesday, March 11, 2014
TMT labeling video
As a hint of things to come, check out the TMT 6 plex consumable site. It now includes an instructional video for how to perform TMT labeling.You can view it he...
Monday, March 10, 2014
Do you love FASP?
I love FASP (filter aided sample preparation). How can you beat easy, clean digestions? What about with Enhanced FASP?This paper from Erde et. al., takes aim at improving FASP and comes up with a 300% increase in peptides! Check...
Sunday, March 9, 2014
Comparative proteomic analysis reveals characteristic molecular changes accompanying the transformation of nonmalignant to cancer lung cells
Interesting paper from Li Zhang's lab. Straight up comparison between two cell lines from the same patient -- a normal cell line and a lung cancer cell line. iTRAQ labeling and Q-TOF for analysis isn't the most sensitive way of doing things but...
Thursday, March 6, 2014
Intro to mass spectrometry videos from freelance teacher.com
I've used this comic from "Toothpaste for Dinner" before, but I still like it.I stumbled across this guy, today, he has a site called "FreeLance Teacher" and he films himself in front of a chalk board explaining chemistry, physics, and mass spectrometry....
Monday, March 3, 2014
MS-Viewer -- Powerful new tool for Protein Prospector
An awesome new tool is up on the Protein Prospector and is detailed in this paper, currently in press (and open access) at MCP.The MS-Viewer takes aim at a lofty goal -- a program that can open post-processed shotgun proteomics data from different sources...
Saturday, March 1, 2014
Blogger hates histograms -- or a study on the distribution of ions selected for fragmentation on an Orbitrap
Whats this weird thing, you ask? Well, this is a histogram. And blogger apparently hates histograms, cause I've tried everything and this is the only way it will display.Misconception? If we digest a whole cell lysate with trypsin,...
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