Shared Proteomics Interviews -- Mike MacCoss and Josh Coon

SharedProteomics has made a habit recently of interviewing some of the top innovators in our field. Their collection of interviews is now something that can be reached directly from the home page.  The most recent additions have been Josh Coon and Mike MacCoss.  You can read about these and other names we all know here.

SympatiQCo

Automated quality control analysis of accumulated RAW data?  Am I sleeping?  After years of dreaming about quality control being taken seriously in Proteomics, the last year has been a revelation!  People all over the place are talking about great things like the PRTC (Peptide retention time calibration) standards from Pierce and new software is whispered about all over the place.

But this one is real and from (who else?) our friends at IMP and the Austrian Academy of Sciences.  SympatiQCo is the product of Michael Mazanek and is meant to be a server based system to automatically QC your LC-MS runs.  It looks at peak shape, retention time and can even perform Mascot test searches if a server is available.

Definitely go here to find out more!

Is ProteoIQ going the way of Elucidator?

Back in May, ProteoIQ suddenly became the property of Premier Biosoft.  I generally let news like this slide by, mostly because I want to stay out of it.  This week, however, I learned from several customers that the changes haven't been entirely favorable.  Both customer service and technical support seem to have taken a hit in the move.  Hopefully Premier will get it together and not let this nice software package go the way of the now legendary Elucidator suite!

R for Proteomics

Nothing makes me happier when rigorous statistical analyses are applied to genomics and proteomics data sets.  That is why I had to do a serious double-take when I was informed about R for Proteomics.

If you aren't aware, R is an open source statistics platform that is supported by a large community of programmers and scientists.  It is used in everything from population dynamics to microarray studies.  The real flexibility in R is gained by the fact that small programs can be relatively easily integrated into R as it has no problem with programs written within its own sub-language or C or C++.  The real power comes from the fact that the community actually develops new programs for it and supports them.

R for Proteomics is a smaller sub-branch that is beginning to gain some steam.  A new review by Laurent Gatto and Andy Christoforou is currently in press at Elsevier that highlights some of these programs and their capabilities.  And there are many, and all of them adhere strongly to the core philosophy of R, that robust statistics come first.

For more information, follow this link.

Phosphoproteomics of Type 4 Pilus construction

When I was in graduate school, I heard a LOT about the construction of Type 4 pili.  This was because I worked down the hall from one of the top Myxococcus labs in the world.
So when I was digging through the papers in press at MCP and I saw this new one that deals with the phosphoproteomics of Type 4 pili construction, it caught my eye.

The subject of the paper is a thermophilic bacteria that uses Type 4 pili to get around.  The authors use titanium dioxide to enrich for phosphopeptides from the bacteria while it is moving under different high temperature conditions.  An Orbitrap XL does the grunt work and helps identify the key phosphorylation sites for this strange and interesting organism.

The paper is the result of work at several top universities in Taiwan and good  read for any of my microbiologist friends out there!

Book recommendation

This is somewhat on-topic, but also kind of a distraction.  I've nearly finished this book and I highly recommend it.  We are seeing this term "Big Data" everywhere.  From the covers of the best academic journals to those of magazines in the airport bookstores, we're surrounded by this term.  This book provides a really good explanation of what this really means.  While the examples they use are for everyone, like how the Amazon recommendation engine works and how Google tracks the spread of the flu, I'm sure you'll find yourself thinking of ways to apply these concepts to our field.

Big day for the blog!

This is a big day for the blog.  The staff has doubled.  Santosh Renuse of the Institute of Bioinformatics in Bangalore has joined in my efforts here and will be a contributing author.  I hope these changes will help to move the blog into more of what the title says it is:  an outlet for News in Proteomics.  Sometimes I feel that I get too caught up in specific applications to keep a good eye on the major new advances in our field.  With double the contributors I think we'll have a better chance of making this what I've always hoped it could be.  I expect some exciting changes.

Chorus Project -- My favorite thing from ASMS 2013!

The Orbitrap Fusion is awesome.  The releasing of the most sensitive triple quads of all time is a great advance for everyone.

My personal favorite thing to come out of ASMS 2013, however,  is the Chorus Project.  I`m going to rant for a second on why that is.

A few years ago this extremely prestigious genomics researcher at Duke got busted for faking genomics data.  Not small time faking, BIG TIME faking.  He had convinced people that his microarrays and analysis techniques were so accurate that he could do cDNA microarrays on patients and tell what chemotherapy would work best for their cancer.  And people were doing it!

Of course, it didn`t start there.  It started with several completely fabricated studies that had made it to the very very best journals.  And they made it because the array data was just too big and dense for anyone to manually review.

Almost all genomics journals require the dropping of genomics data into repositories for just this reason.  We had the same thing in proteomics.  You couldn`t publish in MCP until your data was up on Tranche.  Unfortunately, our data kept getting better and that meant bigger, and now Tranche can not handle even a fraction of the proteomic data being published.

We currently have no oversight.  We can publish anything, and there have been a few papers recently (no hints on which, what, or who) that have had findings that are a little beyond belief.  We are currently at a point where our field can be seriously hurt by liars and charlatans and there has been no solution in site.

Enter the Chorus Project.  Proteomics processing and data sharing viewing through the Cloud.  Cloud sized storage that can handle even the next generation platform data files  AND proceess them (Comet processing on the cloud!) AND make the data easily viewable from any web connection.  You see the data without having to download all 700 GB of it.  It is incredible.

Disclaimer:  It is still in Beta version, but it is coming.  I have been on it (Beta tester! Woo!), and I have seen it run.  I dream of a day when I can read a paper with amazing new findings that push the boundaries of my belief and logging onto Chorus and seeing it right there and being able to believe it!

I know you want to know more about Chorus and the great minds who are bringing it to us.  So go to https://chorusproject.org and check it out!

Top10? Top20? Top30? What experiment do you run on the Fusion?

I know I touched on the Fusion a little, right before I left.  But I just want to touch on one of the coolest features of the instrument, called Dynamic Scan Management (DSM).

If you've been following my blog, you know that I've spent considerable time providing my recommendations for optimizing LC-MS parameters with the appropriate number of MS/MS events.

DSM negates part of this.  Due to the architecture of the Fusion, it can, like the hybrids collect MS/MS scans while the MS1 is running.  Unlike the hybrids, however, the Fusion will automatically perform the maximum number of MS/MS scans that can be during the MS1 fill and acquisition time.  This way you get the highest possible number of MS1 and MS/MS scans for every experiment at your particular resolution.  And, BTW, thanks to HCD ion trap scans, the Fusion can get as many as 20 scans/ second!

I have spent a week working with 2 Orbitrap Fusion models at the San Jose demo labs and I can promise you that this thing is a big step forward from the hybrid systems, definitely in part due to DSM.  On top of that, not having to optimize your MS/MS to your LC and sample complexity really takes some of the guesswork out of setting up each experiment.  I hope to have some data to show later on samples ran on an Orbitrap Velos Pro followed by a run on a Fusion in the next few days.

Bloggers needed!

I came to a sudden realization yesterday.  I don't think I can do this alone anymore.  I really want to keep this going, but sometimes I'm going to take 3 weeks of vacation starting in the middle of ASMS and am going to get behind on everything.
So, I decided that I am willing to start opening up this blog to other writers.  Over the years I've had a request or two, but I had more spare time and wanted complete control over this forum.  If you are interested in contributing, drop me a line at: orsburn@vt.edu.  Let's keep this thing rolling.
Even if no one else jumps on, there is just SO much for me to write about right now.  Expect a lot this week (once my new laptop arrives tomorrow, that is!  I'm also having some technical difficulties, btw!  Double excuse!)