[BiO BB] question on processing LC/MS data

Safee safee.ullah at gmail.com
Fri Apr 7 01:00:22 EDT 2006


Hi James,

The Sashimi website at http://sashimi.sourceforge.net/ offers a collection
of converter programs for some common mass spectrometer file formats.

Try to find Waters QTOF in that list..

Regards
safee ullah



On 4/7/06, James Anderson <janderson_net at yahoo.com> wrote:
>
> Hi,
>
>    I am now working on some LC/MS data (the machine is made by
>
> Waters). I have the raw data file, each sample has very large size (in the order
>
> of several G bytes). Each file has 3 functions and each function has a lot
>
> of scans with each scan corresponding to a retention time. I have 6
>
> control samples and 6 dosed samples, the purpose is to find those proteins that
>
> are differentially expressed between the two groups (control and dose).
> The data is the raw txt file produced by Water Q Tof. However, I don't know how
> to convert those txt files to NetCDF or mzXML format which could be processed
> by some software. In addition, the format of each sample is
> as follows:
> Each sample has 3 functions.
> Function 1. Full scan data
> Function
>  2. Cell collision voltage data, this is developed by Waters to identify peptides.
> Function 3. Lock mass data, which is used to calibrate the spectrum.
> Does anybody have similar experience processing this kind of data?
>
>
>
>    Many thanks.
>
>
>
>    James
>
>
>
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