Archive | June 2013

Linux on VM!

I wonder why many software programers like Linux. I like it too. I think the greatest thing about Linux is free on top of its stability. For me, linux shell scripting allow automation of many processes required for bioinformatic analysis. For someone who wants to start using Linux, using virtual machine is a great way to start. You don’t have to worry about partitioning of the drives and file transfers are pretty easy once it is set up.

Installation of VM can be done from here. Click the download on the left panel, and select your operating system. Installation should be straight forward. Once you installed VM, you need to select what kind of operating system you want to use.  In this case, I pick ubuntu for Linux OS.  Then you need to set up memory, storage space, CPU (threads) and etc. You can play around, but what is most important is to mount the CD/DVD drive correctly with image file. Let’s get the file first.

Here you can download the latest ubuntu.

http://www.ubuntu.com/start-download?distro=desktop&bits=32&release=latest

If you click the link, your browser (most likely) starts downloading image file (iso) for the latest ubuntu. You need to unzip this big file (800MB). I use  7-zip to extract files (it is free).

Then you can move this iso file wherever you want-, I would put it in somewhere in VM directory. Next you need to mount the image file on your CD/DVD drive for your new ubuntu. This part is essential. If you don’t do it right, you see this error message.

Screen Shot 2013-06-30 at 4.42.14 PM

In order to mount your drive correctly, first you go settings on your VM, and select storage. You will see controller:IDE and Controller:SATA.

Screen Shot 2013-06-30 at 4.38.25 PM

If click the controller: IDE, you see two + buttons at the bottom of the screen. Click the left + button, then select Add CD/DVD drive. It will ask if you want it to leave empty or choose disk. So select choose disk, then locate the iso file you saved.  If this part is done correctly, you should see the .iso file in the controller:IDE box.

Screen Shot 2013-06-30 at 4.39.40 PM

OK, you are almost done. Now you hit ok, and then start the ubuntu. The VM will start the new OS and installation window appears. Congratulations! The installation of ubuntu should be straight forward, so I will not discuss about it here.

Screen Shot 2013-06-30 at 4.30.53 PM

PeptideShaker Database Requirements (0.22.4 or earlier)

PeptideShaker likes specific format for database if you don’t use searchGUI. They recommend Uniprot database. But occasionally I want to use my own database. There are two specific requirements for correct database in PeptideShaker.

1) It needs decoy sequences.

2)Accession number for decoy sequence has “_REVERSED” tag.

For 1), if you don’t contain decoy sequence, it complains “No Decoys Found”.

decoy-not-found

For 2), if the tag is not correctly added, no unique accession error appears.

Picture1

So the correct fasta format for PeptideShaker is

>IPI000123456.7:protein_description
MEHKEVVLLLLLFLKSGQGEPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKC
EEDEEFTCRAFQYHSKEQQCVIMAENRKSSIII

>IPI000123456.7_REVERSED:protein_description
MEHKEVVLLLLLFLKSGQGEPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKC
EEDEEFTCRAFQYHSKEQQCVIMAENRKSSIII

These requirements are a little bit problematic. I also use IDPicker for MS/MS spectra analysis and it uses decoy tag before the accession number. Well, all I have to do is to create two databases and search with different databases for IDPicker and PeptideShaker.

If you are using searchGUI to search your MS/MS spectrum with OMSSA & X!tandem, you don’t have to worry about these requirements. The software will take care of them.

What to write?

Hello world! This is my first blog and I am hoping to continue for long time. I have been thinking about what to write, or what to blog about for two years. Now I think I know what to do. I am a scientist who runs mass spec everyday. I have probably run over 5000 samples already… some of them are mine, the others are from the others.

Mass spec is really a cool instrument-, so sensitive and accurate to identify or quantitate ions. But because there are so many different molecules on earth, we have unlimited way of using mass spec.

After running so many samples, I realized that it is hard to organize what I have run. I know what was run, and I kept logs on the computer. But I wasn’t sure what I actually learned from these samples well.

So I decided to write something about what I found from the work I do everyday. Especially about analysis of mass spec results because there are so many ways to analyze and make sense out of them.

What I am hoping is to exchange some ideas with other people with similar interests to boost my ability to analyze mass spec data.  So let’s get started!!!

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