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 RAW data and gives you an idea of how you should be setting up your searches.  I had heard about it, but never used it.  Now it is a node that you can buy from Protein Metric for PD.

This is how it works:  I have a RAW data file that I know comes from a human tumor cell lysate.  I know that this tumor is all screwed up (its cancer cells, its gonna be screwed up) but I don't know how screwed up.  So I take the RAW file and I run it through Preview.

I tell Preview what I know about the file:
Or whatever I feel like.  Sure, I could check it to see if its CID or HCD, but lets let Preview figure it out.  Do you see what is under Search Options?  Below the insanely awesome toggle where you tell it whether you have Phospho Enriched?  Wild card search!  This is the same wild card search that is in Byonic, but you have a little less control over the mass ranges.  They are preset.

In 4 minutes (140 minute Elite run with ~50,000 MS/MS scans on my quad core laptop with SSD buffered hard drive....this software is very very fast.  How fast?  Faster, even, than Morpheus on this PC) you get something like this:

This sweet overview of the file opens in your default browser.  It gives you your top scoring proteins and your potential m/z errors.  You can use that data to fine tune how you set up your real search.

That isn't all.  You get several other HTML pages generated with more details AND you get an Excel sheet with potential wild card results.

In the case of this file, the Excel sheet pointed out that I should definitely search for methionine oxidation AND it pointed out a slew of peptides that have a +128 Da mass shift.  Interestingly, there really isn't anything of that mass in Unimod.  Is it the next -ome that we have never looked at that is disregulated in tumors?  We won't know until we take a look.  And if we figure out what it is (or not, and just search for it anyway) I can use the new ptmRS to get confident site localization of the mod!

To find out how you can get Preview, follow this link to the Protein Metrics home page.  There is much much more to come.  After I get some real work done I'll show you the awesome stuff that I'm getting out of the Byonic node!

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