TMT analysis with Libra?

[Ruby]

Has anyone ever used Libra to analyze TandemMassTag (TMT) data
acquired on an Orbitrap? I'm using the TPP via the SageN/Sorcerer
interface, and would love it if someone could tell me what the command
line would be appropriate for the "Xinteract options".

Thanks!
Rebekah

[Luis Mendoza]

Hello Rebekah,
I have not heard of anyone using Libra on TMT data, but it should be able to handle it.

You will first need to generate a Libra condition file, where you specify some options as well as isotopic contributions to each channel.  (more info here:  http://tools.proteomecenter.org/wiki/index.php?title=Software:Libra  and here:  http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html ).  I am not familiar with the Sorcerer interface, but recent releases of the TPP GUI have a screen where you can generate this file (under Utilities -> Libra Conditions). The interface has a drop-down that will pre-populate the channel masses, though you will nee to enter the isotopic contributions to neighboring channels (or leave them at zero).

The condition file is the only other input required for Libra, so just specify it by name in the interface, and you should be good to go.

Hope this helps.  Let us know if you have any other questions, and please report back on your TMT experience with Libra.  We would like to get a hold of the "standard" isotopic contribution factors so that we can include them as defaults in the GUI.
--Luis

[Ruby]

Ok. Thanks for the help. I'll let you know what I find during the
analyses.
-Rebekah

On Jan 29, 1:42 pm, Luis Mendoza <lmend...@systemsbiology.org> wrote:
> Hello Rebekah,
> I have not heard of anyone using Libra on TMT data, but it should be able to
> handle it.
>
> You will first need to generate a Libra condition file, where you specify
> some options as well as isotopic contributions to each channel.  (more info
> here:  http://tools.proteomecenter.org/wiki/index.php?title=Software:Libra

> and here:http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom...).

>  I am not familiar with the Sorcerer interface, but recent releases of
> the TPP GUI have a screen where you can generate this file (under Utilities
> -> Libra Conditions). The interface has a drop-down that will pre-populate
> the channel masses, though you will nee to enter the isotopic contributions
> to neighboring channels (or leave them at zero).
>
> The condition file is the only other input required for Libra, so just
> specify it by name in the interface, and you should be good to go.
>
> Hope this helps.  Let us know if you have any other questions, and please
> report back on your TMT experience with Libra.  We would like to get a hold
> of the "standard" isotopic contribution factors so that we can include them
> as defaults in the GUI.
> --Luis
>