Proteome Discoverer 1.4 on a server

I get this question a lot, get the answers mixed up, and wonder "why haven't I just posted this on the blog where I can find it?"

Solution!

Can I install PD 1.4 on a Windows Server?
Answer: Yes!  People all over have PD 1.4 running on their servers.  We know that it works for sure on Windows Server 2008 and Windows Server 2012.

We also know that PD 1.4 works well with multiple cores.  It appears to work best, however (according to anecdotal evidence) when up to 24 cores are being used.  I have heard of two situations (which, honestly, may have been the same situation, I just heard it from different people) where devoting more cores from a cluster to run PD 1.4 didn't improve speed the way we might expect.  For example, 48 threads from the cluster weren't twice as fast as 24 threads from the cluster (maybe it was 80% faster, I don't know, but I've heard that it wasn't 2x, thats all).  But I only run 4 threads on my laptop and on my team's server.  And I can knock out a 1.5GB RAW file with 3 dynamic mods in 6 minutes (SSD buffers..woooo!) so 24 threads sounds hella fast to me!

Keep in mind that PD 1.4 is a couple of years old now.  Maybe there will be a new version soon!

READ MORE - Proteome Discoverer 1.4 on a server

This has to be posted.

I'm working on something to post that I think is super cool, but its going to take me a couple of days to get it.  Please accept this filler PUG PUPPY entry for today.

READ MORE - This has to be posted.

PIR -- Another cool protein database

Something I consider a major goal for proteomics?  Moving from gene ontology (GO) analysis of our datasets to true PRO (protein ontology).  Genes are great.  Grouping genes by functional categories is also great.  But proteins are what we study and there is a point where we don't have a complete overlap.  Consider the number of proteins out there vs the number of unique gene identifiers.  WAY more proteins than genes to correlate them to.
 Protein Center is making leaps and bounds all the time toward bridging that gap.

The Protein Information Resource (PIR) is an additional resource that focuses on true PRO.  For example, unique identifiers exist for various known cleavage events of gene products.  If we have the whole protein or half the protein, do they do the same thing? Probably not.  And it sure would be nice to know which one is present, right?

You can check out the PIR here.

Another find by Alexis.  May need to put her down as a contributor to the blog!

READ MORE - PIR -- Another cool protein database

Caspases can be regulated by protein phosphorylation

Caspases are proteins that chew things up.  If you didn't know better, they look like they chew things up completely indiscriminately -- every protein gets chopped up.  This is really useful for controlling diseased cells during things like apoptosis.  This cell is bad, program cell death, destroy everything.

This awesome new paper in this month's MCP from Jacob Turowec et al., (permanently open access!) shows that caspase cleavage may not be indiscriminate at all.  In fact, it may be regulated, while it is happening, by protein phosphorylation.

To decipher this, the team employed an unbiased n-terminal approach they call TAILS and analyzed the rate of degradation of proteins in caspase activated systems.  The analysis was performed on an Orbitrap Velos and the data was analyzed with MaxQuant.

They find that some phosphorylation events lead to increased cleavage rates and some lead to decreased rates.  Interesting, right!  It seemed strange that we would just auto-self destruct cells indiscriminately.  Even in this worst case scenario, it appears that we have some measure of control after all.

I stole this image from their paper because its cool and describes their aproach.

READ MORE - Caspases can be regulated by protein phosphorylation

Free training courses from EMBL

There just isn't a good excuse these days to not know stuff. Its too easy to learn about anything you want!

For example, wanna take free classes in:

Metabolomics
Next gen sequencing
Genomics
Protein interactions
PROTEOMICS
or
Reactomics (whatever that is?)
and so on..and so on...

Follow this link to EMBL and check it out!

READ MORE - Free training courses from EMBL

To deplete or not to deplete...part 7 or something....

Plasma protein depletion?  So many opinions out there!  How about another one?  How about the most cited paper from Open Proteomics!?!

Proteomics of human plasma: A critical comparison of analytical workflows in terms of effort, throughput and
outcome, is that paper.  (Open access! Wooo!)

In this one, the authors take a serious run at the pluses and minuses of depletion (like what a HUGE protein loss they take with depletion...quantified! from different depletion techniques).  Then they take the depleted, undepleted, etc., and run it all out on an Orbitrap Elite using the same settings.

The results?  Well, thats a surprise.  Its open access and they made some nice Venny Venn Diagrams.  Worth checking out! (and easier to take seriously than David Tennant doing Hamlet!)

READ MORE - To deplete or not to deplete...part 7 or something....

HPRD -- A protein database from the Pandey lab

I've known about this one for quite a while, but I just realized I don't have anything up on the new blog (and I never fully transferred everything I've written from the old one...and probably won't at this point, lol!)

The HPRD is another cool protein database that is a joint effort from the Pandey lab and the Institute of Bioinformatics.

Check out the output here on ITGA5:

Quick reference info at the top:  class, GO function and process:  followed by a quick graphical breakdown of what we know of the protein at this point.

Followed up with info on pseudonyms for the protein, substrates, etc.,

You have other options as well, such as looking up canonical pathways.  In a minor criticism, the pathways come up in HTML as a list and must be downloaded for viewing/linking.  I definitely prefer when KEGG or ball and stick pathway models pop up, but I can get those from other sites.  Those other sites won't give me graphical breakdowns of my protein domains, and I think this is the real advantage of this site over other ones out there.

You can link directly to the HPRD here.

READ MORE - HPRD -- A protein database from the Pandey lab