[BiO BB] question on processing LC/MS data

Ilya Venger ilya.venger at weizmann.ac.il
Sun Apr 9 03:16:32 EDT 2006

Hi James,
what software is used to acquire the data? It is possible that the same 
software has a plugin or an option to convert the files. Most probably 
the conversion will be to NetCDF. Did you try going to the sashimi 
project page and looking for the software there?


James Anderson wrote:
> Hi, llya
>   Thanks for your email. Unfortunately, we don't have Waters Masslynx 
> software. I asked some people in this field, they said that Masslynx 
> can convert those raw files (binary file) to mzXML. However, the raw 
> data we have is not binary file, it is txt file. I don't know how to 
> deal with this.
>   Thanks.
>   James
> */Ilya Venger <ivenger at wisemail.weizmann.ac.il>/* wrote:
>     Hi,
>     If you have Waters QTOF you might also have the MassLynx software. You
>     can use the program "databridge" that comes with the Waters Masslynx
>     software (it can be found in the "start" menu in the same tab
>     where the
>     MassLynx is). It is a converter between the different file formats. It
>     will produce more than one file, the biggest one contains the relevant
>     data.
>     If you have any more question don't hesitate to ask.
>     Ilya
>     >>> janderson_net at yahoo.com 04/07/06 6:10 AM >>>
>     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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