Thermo SMART digest kits

Recently, I've been hearing a lot of good things about the Thermo SMART digest kits, but I hadn't had time to really pay attention. They did sound a little bit like the Perfinity digest kits.  Turns out, they are more than a little similar!

Found this tidbit that explained the similarity in my LinkedIn feed!

Potential urine test for pancreatic cancer!!!!

This is AWESOME!  I saw people discussing it on Twitter a while back but hadn't had a chance to investigate.  How big of a deal is it?  Well, its such a big deal that a writer for CBS in the U.S. was actually assigned to write a page on it!  And if you follow U.S. television "news" you know that it takes something BIG for them to devote an instant to something unrelated to the Kardashians.

Check this out:

We have virtually no early detection systems for pancreatic cancer. Typically you go in with severe back pain and THEN you find out it has progressed like crazy and you have months to live. Its a disease bad enough that it can take even this guy out...

...a mere 20 months after his diagnosis...  Which is typical.  Only around 6% of people who are diagnosed are alive 5 years later.  And we may have a functional biomarker IN URINE!!  All signs point to it being a beatable cancer, if you catch it in time, we just never do!  What if early detection was part of your normal hospital panel when you get your physical every year?  You catch it before it is terrible, and you and your capable oncologist beat it, that's what!

How'd they find these biomarkers?  By LC-MS/MS of course.  LC-MS/MS by the capable hands of the great team at MSBioworks, no less.

Here is the BBC article.
Here is the original journal article abstract at Clinical Cancer Research.

Keep this one in your back pocket the next time some know it all says that proteomics and mass spectrometry aren't living up to their promise!  Get back to work you awesome people and

Does your Proteome Discoverer interface look weird? Side effects of Windows "Magnifier Tool"

For the last several weeks the Proteome Discoverer interface on my PC has looked kind of terrible. The icons are big and easy to see, but I can't put a workflow on a single page.

Turns out, there is an option in your Control Panel in Windows 7-10 that can have big effects on the viewing of the PD interface and its called the Magnifier tool.  If it (somehow?) gets moved up to medium it'll make it really hard to have the entire Consensus menu open and still be able to see the Post Processing nodes.

Probably this won't happen to you, but just in case!  (It was driving me kind of crazy!)

Genome analysis suggest that Pugs may not be from Asia!

I would like to divert you from proteomics to a fantastic study of dog genomes.

In this paper in some journal called "Science..." some brilliant people tricked some funding agency into giving them money to sequence a ton of single nucleotide polymorphisms (SNPs) from a bunch of dogs.  OF COURSE, one that they would focus on would be the grand and majestic Pug.

The story has always been this -- that Pugs originated with other normal-faced dogs somewhere in Asia. This is substantiated by old art that seems to show Pugs in early Chinese dynasties...except those Pugs look like Shar Pei...

Okay. So, the genomics might be solving all sorts of questions.  The big question, though, still stands. Where did the greatest dogs in world history come from?

I think we need to go all Robert Langdon on it to figure it out.  What are the conspiracies surrounding Michelangelo?

How to automatically download FASTA files in Proteome Discoverer 2.0

Starting in Proteome Discoverer 2.0, we now have the ability to directly download FASTA databases from ProteinCenter.  However, it might look a little confusing if you select that option from your FASTA file menu in Administration.

What you need is your Taxonomy ID.  For example, if you want to autodownload all the SwisProt entries that ProteinCenter has for our species you'd want to use code 9606 and click the Import button.

How do I find these Tax IDs?  I use this thing!

This is the NCBI Taxonomy Browser (click here for direct link!). Just put your species name in the top and it'll come back with your organism and the Tax ID at the top.

There are several other such tools available on the web, but this is a quick and easy one.

Important note if you use this tool: Once you download a FASTA from ProteinCenter, you now have the ability to search for updates when ProteinCenter posts them. If it finds one it will directly copy over the FASTA you have in place. If you are in a role where you need to keep a constant record of where you obtained your FASTA and when, it might be easier to download them yourself the old fashioned way so you can keep a time stamp  and record of each individual FASTA.

Shoutout to Brad for pointing out that this process could use some clarification!

I forgot to check on the EPD in a while!

Wow. We have so many resources out there these days that I honestly can completely forget about some of them (and get them mixed up with others).  One that I hadn't thought to check on in a while is the Encyclopedia of Protein Dynamics.  Thanks to Twitter (@PastelBio, w00t!) and the fact that I'm too lazy to leave my hotel tonight, I can check out and direct you to a cool tool on the site.

Now, as a disclaimer, the tools at the EPD should have little trademark symbols by them. Unfortunately, I do not know how to draw such things.  So, all of the tools I'm about to mention are the property of the licensed, trademarked EPD project at the Lamont lab. All the normal stuff applies for such things, and you have to agree to use cookies if you want to use the site.

The tool I want to direct you to is the PepTracker (trademarked!). The PepTracker gives you information about your protein of interest, including:

Protein turnover (and half-life plots!)
Abundance
GO information
Linked proteins (like that awesome string map at the top! publication ready, with permissions, of course!)
Localization in certain cell lines
Heatmaps of proteins that cluster with your protein-of-interest
Cell cycle information
And other stuff!

Really really cool tool and handy information all in one place!

Directly search expressed sequence tags with Mascot

Cool tips in this month's Mascot Newsletter for those of you who are studying weird things that haven't gotten fully annotated genomes.  Search with your MS/MS data against Expressed Sequence Tags (EST).  The newsletter highlights one fish that only has 1,200 annotated proteins but nearly a quarter-million ESTs.  Sure, its more work for you to sort it out, but it beats only coming up with 1,200 proteins and they'll annotate it all someday!