[BiO BB] question on processing LC/MS data

James Anderson janderson_net at yahoo.com
Thu Apr 6 23:10:24 EDT 2006


   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.


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